Variant report

Variant	rs2335937
Chromosome Location	chr4:1321516-1321517
allele	A/C
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	chr4:1319288-1323843	K562	blood:	n/a	n/a
2	POLR2A	chr4:1321455-1321836	K562	blood:	n/a	n/a
3	POLR2A	chr4:1320910-1321688	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:1300397..1304694-chr4:1319400..1323043,4	K562	blood:
2	chr4:1313294..1315156-chr4:1320127..1321902,2	MCF-7	breast:
3	chr4:1317445..1321964-chr4:1322066..1326605,8	MCF-7	breast:
4	chr4:1282015..1284359-chr4:1319933..1321825,2	MCF-7	breast:

Variant related genes	Relation type
MAEA	TF binding region
ENSG00000090316	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10000012	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs10000797	0.87[ASN][1000 genomes]
rs10006381	0.87[ASN][1000 genomes]
rs10012416	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10012819	0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10018133	0.87[ASN][1000 genomes]
rs10018627	0.87[ASN][1000 genomes]
rs10024529	0.87[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[ASN][1000 genomes]
rs10025954	0.87[ASN][1000 genomes]
rs10029534	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032327	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11933854	0.80[EUR][1000 genomes]
rs11933855	0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs1250129	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12639938	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12646130	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1680032	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs1732115	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2101094	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs28412861	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28429103	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28437782	0.87[ASN][1000 genomes]
rs28477912	1.00[ASN][1000 genomes]
rs28515563	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540746	0.87[ASN][1000 genomes]
rs28647383	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649968	0.87[ASN][1000 genomes]
rs28678404	0.81[ASN][1000 genomes]
rs28711287	0.87[ASN][1000 genomes]
rs28712208	0.80[EUR][1000 genomes]
rs3817604	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs5013707	0.80[EUR][1000 genomes]
rs58750335	0.87[ASN][1000 genomes]
rs59810282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60722337	0.86[EUR][1000 genomes]
rs6845586	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847321	0.86[CEU][hapmap]
rs73073737	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs730830	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs7654152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7659916	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	nsv461157	chr4:1300077-1352685	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
22	nsv593301	chr4:1300077-1352685	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
23	nsv878346	chr4:1300077-1363886	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
24	nsv878347	chr4:1300077-1866358	Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
25	nsv878348	chr4:1305269-1386570	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
26	esv1833544	chr4:1305962-1327941	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
27	esv1794294	chr4:1307119-1817474	Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
28	nsv980177	chr4:1317488-1323519	Genic enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
29	nsv878349	chr4:1318132-1363886	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
30	nsv878350	chr4:1320023-1500753	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2335937	MAEA	cis	Thyroid	GTEx
rs2335937	CRIPAK	cis	lymphoblastoid	seeQTL
rs2335937	CNR1	trans	lymphoblastoid	seeQTL
rs2335937	KIAA1530	Cis_1M	lymphoblastoid	RTeQTL
rs2335937	KIAA1530	cis	cerebellum	SCAN
rs2335937	CRIPAK	Cis_1M	lymphoblastoid	RTeQTL
rs2335937	CRIPAK	cis	cerebellum	SCAN
rs2335937	CRIPAK	cis	parietal	SCAN
rs2335937	KIAA1530	cis	parietal	SCAN
rs2335937	HAUS3	cis	cerebellum	SCAN
rs2335937	CRIPAK	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1303600-1339400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:1305000-1327200	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr4:1305200-1326600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:1305200-1330200	Weak transcription	Fetal Heart	heart
5	chr4:1306000-1323400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr4:1306200-1322200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:1309200-1330400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:1310800-1321800	Strong transcription	Primary T cells from cord blood	blood
9	chr4:1310800-1323200	Weak transcription	Psoas Muscle	Psoas
10	chr4:1311800-1322400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:1312200-1321800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr4:1313600-1335600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:1314800-1323200	Strong transcription	Fetal Muscle Leg	muscle
14	chr4:1314800-1328200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:1314800-1335200	Strong transcription	Dnd41	blood
16	chr4:1315000-1325000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr4:1315000-1335600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:1315200-1322600	Strong transcription	Esophagus	oesophagus
19	chr4:1315200-1323400	Strong transcription	Placenta	Placenta
20	chr4:1315200-1324000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:1315200-1335400	Strong transcription	Fetal Brain Female	brain
22	chr4:1315200-1335600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:1315200-1335600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:1315200-1335600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:1315400-1321800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:1315400-1322000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr4:1315400-1322000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:1315400-1322400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:1315400-1323000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:1315400-1323000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr4:1315400-1325200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:1315400-1328400	Strong transcription	Adipose Nuclei	Adipose
33	chr4:1315400-1329400	Strong transcription	Colonic Mucosa	Colon
34	chr4:1315400-1331800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr4:1315400-1332200	Strong transcription	Fetal Intestine Small	intestine
36	chr4:1315400-1335200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:1315400-1335400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr4:1315400-1335400	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr4:1315600-1325200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:1315600-1325400	Strong transcription	Brain Hippocampus Middle	brain
41	chr4:1315600-1325800	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr4:1315600-1328200	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr4:1315600-1335400	Strong transcription	Brain Germinal Matrix	brain
44	chr4:1315600-1335600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:1315800-1322200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr4:1315800-1322400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:1315800-1322400	Strong transcription	Brain Angular Gyrus	brain
48	chr4:1315800-1331800	Strong transcription	Fetal Intestine Large	intestine
49	chr4:1315800-1333400	Strong transcription	Fetal Stomach	stomach
50	chr4:1315800-1335200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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