Variant report

Variant	rs2101094
Chromosome Location	chr4:1235643-1235644
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:1234455-1238081	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:1235151-1235647	GM12878	blood:	n/a	n/a
3	POLR2A	chr4:1235340-1235700	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:1235378-1235962	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:1215883..1221793-chr4:1233494..1238232,6	K562	blood:
2	chr4:1233604..1236548-chr4:1385152..1387591,2	K562	blood:
3	chr4:1235141..1249133-chr4:1336906..1347308,118	MCF-7	breast:
4	chr4:1233077..1236112-chr4:1282661..1284848,3	MCF-7	breast:

Variant related genes	Relation type
CTBP1	TF binding region
ENSG00000179979	Chromatin interaction
ENSG00000159692	Chromatin interaction
ENSG00000090316	Chromatin interaction
ENSG00000163945	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10000012	1.00[JPT][hapmap]
rs10024529	1.00[JPT][hapmap]
rs11247979	0.81[AFR][1000 genomes]
rs1250093	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250096	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250099	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1250100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1250107	0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs1250112	0.84[AFR][1000 genomes]
rs1250115	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs1250116	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs1250121	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1250129	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639938	1.00[JPT][hapmap]
rs12646130	1.00[JPT][hapmap]
rs1265923	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs1680032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1680057	0.85[YRI][hapmap]
rs1732110	0.84[AFR][1000 genomes]
rs1732115	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732117	0.83[AFR][1000 genomes]
rs2004531	0.81[AFR][1000 genomes]
rs2020137	0.81[AFR][1000 genomes]
rs2046151	0.86[AFR][1000 genomes]
rs2335937	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs28429103	0.81[CEU][hapmap]
rs3817604	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs730830	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900013	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900017	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs900019	0.85[YRI][hapmap];0.84[AFR][1000 genomes]
rs900021	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv829835	chr4:1097586-1304239	Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
6	nsv878329	chr4:1147407-1254930	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv461151	chr4:1159680-1236840	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv593277	chr4:1159680-1236840	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv878331	chr4:1159680-1254930	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
11	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
13	nsv461153	chr4:1174861-1254930	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
14	nsv593279	chr4:1174861-1254930	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv461154	chr4:1179213-1254930	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
16	nsv593280	chr4:1179213-1254930	Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
17	nsv878332	chr4:1179213-1254930	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
18	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
19	nsv878333	chr4:1193832-1254930	Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
20	nsv461155	chr4:1203265-1352685	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
21	nsv593281	chr4:1203265-1352685	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
22	nsv1002097	chr4:1212573-1320086	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
23	nsv536986	chr4:1212573-1320086	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
24	esv1811773	chr4:1228251-1287474	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
25	esv1800629	chr4:1228451-1287274	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
26	esv1812851	chr4:1228451-1287274	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
27	esv1823612	chr4:1228451-1287274	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
28	esv1825633	chr4:1228451-1287274	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
29	esv1844406	chr4:1230397-1243775	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
30	esv1836927	chr4:1231363-1244037	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
31	esv1838677	chr4:1231540-1274734	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
32	nsv822433	chr4:1232688-1246206	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
33	nsv878334	chr4:1232910-1254930	Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2101094	MAEA	cis	Nerve Tibial	GTEx
rs2101094	CRIPAK	Cis_1M	lymphoblastoid	RTeQTL
rs2101094	CRIPAK	cis	Whole Blood	GTEx
rs2101094	KIAA1530	Cis_1M	lymphoblastoid	RTeQTL
rs2101094	MAEA	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1204400-1235800	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr4:1204600-1236200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:1204800-1237000	Weak transcription	Psoas Muscle	Psoas
4	chr4:1212600-1237000	Strong transcription	Dnd41	blood
5	chr4:1214200-1236800	Strong transcription	Primary T cells from cord blood	blood
6	chr4:1214400-1236400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:1214400-1238400	Strong transcription	Thymus	Thymus
8	chr4:1214600-1235800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr4:1214600-1236200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr4:1215000-1236000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr4:1215400-1236000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr4:1216400-1236000	Strong transcription	Fetal Thymus	thymus
13	chr4:1216600-1236000	Strong transcription	GM12878-XiMat	blood
14	chr4:1217200-1235800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:1219000-1240200	Weak transcription	Hela-S3	cervix
16	chr4:1221600-1236400	Weak transcription	Fetal Heart	heart
17	chr4:1221600-1240200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr4:1221800-1236400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:1222000-1240800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:1222600-1236000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:1223000-1236600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:1223200-1236800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:1223800-1236200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:1225000-1240200	Weak transcription	K562	blood
25	chr4:1227600-1235800	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr4:1227800-1236600	Strong transcription	Fetal Brain Female	brain
27	chr4:1228000-1236800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:1228400-1240000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:1228800-1236200	Strong transcription	Fetal Stomach	stomach
30	chr4:1228800-1238000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:1228800-1239400	Weak transcription	Fetal Brain Male	brain
32	chr4:1229000-1236000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:1229000-1236200	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:1229000-1236200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:1229000-1237000	Strong transcription	NHLF	lung
36	chr4:1229200-1235800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr4:1229200-1240400	Weak transcription	Fetal Kidney	kidney
38	chr4:1229400-1236000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:1229600-1236200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr4:1229600-1237800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:1229600-1239600	Weak transcription	HSMM	muscle
42	chr4:1230000-1235800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr4:1230000-1238200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:1230000-1240400	Weak transcription	HSMMtube	muscle
45	chr4:1230800-1236400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr4:1231400-1236600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr4:1232000-1237200	Weak transcription	Primary B cells from cord blood	blood
48	chr4:1232600-1235800	Strong transcription	Fetal Lung	lung
49	chr4:1233400-1240600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr4:1233600-1235800	Weak transcription	Stomach Mucosa	stomach

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