Variant report

Variant	rs2293633
Chromosome Location	chr4:1291640-1291641
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	MAX	chr4:1291542-1292061	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr4:1291482-1291999	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr4:1291190-1291674	HepG2	liver:	n/a	n/a
4	TEAD4	chr4:1291505-1291971	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr4:1291541-1291968	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr4:1290513-1292103	K562	blood:	n/a	n/a
7	POLR2A	chr4:1290939-1291735	GM12878	blood:	n/a	n/a
8	POLR2A	chr4:1290789-1292001	K562	blood:	n/a	n/a
9	POLR2A	chr4:1291554-1291895	K562	blood:	n/a	n/a
10	SIN3A	chr4:1291592-1291647	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:1236833..1250005-chr4:1276188..1292579,54	MCF-7	breast:
2	chr4:1241391..1244976-chr4:1289369..1292052,3	MCF-7	breast:

Variant related genes	Relation type
MAEA	TF binding region
ENSG00000159692	Chromatin interaction
ENSG00000196810	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10000874	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10023922	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10024013	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11247984	0.89[EUR][1000 genomes]
rs11247986	0.88[EUR][1000 genomes]
rs11247987	0.89[EUR][1000 genomes]
rs11727167	0.81[EUR][1000 genomes]
rs11730939	0.81[EUR][1000 genomes]
rs12502916	0.80[EUR][1000 genomes]
rs12509700	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12641735	0.89[EUR][1000 genomes]
rs12642396	0.89[EUR][1000 genomes]
rs12642410	0.82[EUR][1000 genomes]
rs13108904	0.83[EUR][1000 genomes]
rs13109112	0.89[EUR][1000 genomes]
rs13112706	0.83[EUR][1000 genomes]
rs13119532	0.83[EUR][1000 genomes]
rs13124383	0.84[EUR][1000 genomes]
rs13128045	0.83[EUR][1000 genomes]
rs13134106	0.83[EUR][1000 genomes]
rs13142772	0.84[EUR][1000 genomes]
rs13149952	0.84[EUR][1000 genomes]
rs1316419	0.89[EUR][1000 genomes]
rs1618072	0.80[EUR][1000 genomes]
rs1620928	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1680072	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1680073	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1680074	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1732099	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1732100	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1732102	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1732106	0.82[EUR][1000 genomes]
rs1732107	0.80[EUR][1000 genomes]
rs1732124	0.80[EUR][1000 genomes]
rs2293634	0.96[EUR][1000 genomes]
rs2293635	0.89[EUR][1000 genomes]
rs28811276	0.80[EUR][1000 genomes]
rs4493484	0.80[EUR][1000 genomes]
rs4974584	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974594	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974596	0.84[EUR][1000 genomes]
rs62293658	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66987549	0.84[EUR][1000 genomes]
rs6826029	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6851528	0.90[EUR][1000 genomes]
rs7668661	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670046	0.82[EUR][1000 genomes]
rs7673398	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7695691	0.89[EUR][1000 genomes]
rs922698	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9631804	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9631805	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9992932	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9992934	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv593298	chr4:1244267-1342521	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
15	nsv461156	chr4:1254930-1312394	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv593299	chr4:1254930-1312394	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv593300	chr4:1272664-1312394	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv878338	chr4:1277826-1358449	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
19	nsv878339	chr4:1277826-1363886	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
20	nsv878340	chr4:1277826-1386570	Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
21	nsv878341	chr4:1277826-1391400	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
22	nsv1002635	chr4:1282603-1402761	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer 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	37 gene(s)	inside rSNPs	diseases
23	esv14797	chr4:1289224-1292044	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv878342	chr4:1291337-1363886	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
25	nsv878343	chr4:1291337-1391400	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
26	nsv878344	chr4:1291337-1414684	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
27	nsv878345	chr4:1291337-1563920	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
28	esv14391	chr4:1291389-1292044	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2293633	CRIPAK	cis	Thyroid	GTEx
rs2293633	UVSSA	cis	Thyroid	GTEx
rs2293633	CTBP1	cis	multi-tissue	Pritchard
rs2293633	UVSSA	cis	Skin Sun Exposed Lower leg	GTEx
rs2293633	CTBP1	Cis_1M	lymphoblastoid	RTeQTL
rs2293633	UVSSA	cis	Whole Blood	GTEx
rs2293633	CRIPAK	cis	Artery Aorta	GTEx
rs2293633	UVSSA	cis	lung	GTEx
rs2293633	UVSSA	cis	Stomach	GTEx
rs2293633	UVSSA	cis	Artery Aorta	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1285200-1293800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:1285200-1303400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:1285400-1293400	Weak transcription	A549	lung
4	chr4:1285400-1294200	Weak transcription	HSMMtube	muscle
5	chr4:1285400-1294200	Weak transcription	HUVEC	blood vessel
6	chr4:1285400-1302400	Weak transcription	Fetal Kidney	kidney
7	chr4:1285800-1296000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:1285800-1302200	Weak transcription	NHDF-Ad	bronchial
9	chr4:1286000-1295200	Strong transcription	Thymus	Thymus
10	chr4:1286200-1293400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr4:1286200-1299200	Strong transcription	Fetal Intestine Small	intestine
12	chr4:1286200-1302400	Weak transcription	Fetal Brain Male	brain
13	chr4:1286400-1299000	Weak transcription	Small Intestine	intestine
14	chr4:1287400-1291800	Genic enhancers	Gastric	stomach
15	chr4:1287400-1292000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:1287400-1294600	Genic enhancers	Spleen	Spleen
17	chr4:1287600-1295200	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr4:1287800-1293400	Weak transcription	HSMM	muscle
19	chr4:1288400-1292200	Genic enhancers	Pancreas	Pancrea
20	chr4:1289000-1296000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr4:1289000-1298800	Weak transcription	Stomach Mucosa	stomach
22	chr4:1289200-1292800	Weak transcription	GM12878-XiMat	blood
23	chr4:1289400-1295200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr4:1289400-1298800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:1289400-1299000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:1289400-1299400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:1289400-1299400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:1289400-1299800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr4:1289400-1302200	Weak transcription	Fetal Heart	heart
30	chr4:1289600-1294800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:1289600-1295400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr4:1289800-1292400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr4:1290000-1291800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:1290000-1292800	Strong transcription	Fetal Muscle Leg	muscle
35	chr4:1290000-1293000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:1290000-1294000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr4:1290000-1294800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:1290000-1295000	Strong transcription	Colonic Mucosa	Colon
39	chr4:1290000-1295200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:1290000-1295400	Strong transcription	Fetal Brain Female	brain
41	chr4:1290000-1302400	Strong transcription	Fetal Stomach	stomach
42	chr4:1290200-1291800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr4:1290200-1291800	Genic enhancers	Esophagus	oesophagus
44	chr4:1290200-1291800	Genic enhancers	Left Ventricle	heart
45	chr4:1290200-1292000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:1290200-1292000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:1290200-1292000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:1290200-1292000	Strong transcription	Fetal Lung	lung
49	chr4:1290200-1292800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr4:1290200-1292800	Strong transcription	Monocytes-CD14+_RO01746	blood

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