Variant report

Variant	rs3802981
Chromosome Location	chr11:5706523-5706524
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	GATA1	chr11:5705710-5706836	PBDE	blood:	n/a	chr11:5706018-5706025
2	JUND	chr11:5705838-5706660	K562	blood:	n/a	chr11:5706370-5706378
3	NFYB	chr11:5706041-5706614	Hela-S3	cervix:	n/a	chr11:5706337-5706352
4	CREB1	chr11:5705845-5706640	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:5705887-5706590	U87	brain:	n/a	n/a
6	POLR2A	chr11:5705798-5706635	GM12892	blood:	n/a	n/a
7	RELA	chr11:5705574-5706758	GM10847	blood:	n/a	n/a
8	FOXM1	chr11:5705761-5706600	GM12878	blood:	n/a	chr11:5706457-5706465
9	POLR2A	chr11:5705807-5706653	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr11:5705881-5706596	U87	brain:	n/a	n/a
11	TBL1XR1	chr11:5705794-5706617	GM12878	blood:	n/a	n/a
12	GTF2F1	chr11:5705621-5706610	Hela-S3	cervix:	n/a	n/a
13	IKZF1	chr11:5705921-5706569	GM12878	blood:	n/a	chr11:5706448-5706460
14	GATA2	chr11:5705806-5706527	HUVEC	blood vessel:	n/a	chr11:5706018-5706025
15	POU2F2	chr11:5705868-5706552	GM12891	blood:	n/a	n/a
16	CREB1	chr11:5705955-5706589	HepG2	liver:	n/a	n/a
17	JUND	chr11:5705917-5706695	SK-N-SH	brain:	n/a	chr11:5706370-5706378
18	EBF1	chr11:5705766-5706649	GM12878	blood:	n/a	n/a
19	CREB1	chr11:5705988-5706579	H1-hESC	embryonic stem cell:	n/a	n/a
20	JUN	chr11:5705823-5706646	K562	blood:	n/a	chr11:5706370-5706378
21	MAX	chr11:5705849-5706678	SK-N-SH	brain:	n/a	n/a
22	SP1	chr11:5705754-5706593	A549	lung:	n/a	chr11:5706376-5706388 chr11:5706376-5706388 chr11:5706059-5706068
23	TBP	chr11:5706009-5706545	H1-hESC	embryonic stem cell:	n/a	n/a
24	SPI1	chr11:5705811-5706528	HL-60	blood:	n/a	n/a
25	POLR2A	chr11:5705818-5706708	GM18951	blood:	n/a	n/a
26	NFYA	chr11:5705932-5706553	K562	blood:	n/a	chr11:5706340-5706358
27	CBX3	chr11:5705719-5706743	K562	blood:	n/a	n/a
28	FOS	chr11:5706123-5706539	MCF10A-Er-Src	breast:	n/a	chr11:5706370-5706378 chr11:5706389-5706400
29	KAP1	chr11:5705725-5706581	HEK293	kidney:	n/a	chr11:5706283-5706291
30	NFYB	chr11:5705959-5706548	K562	blood:	n/a	chr11:5706337-5706352
31	POLR2A	chr11:5706090-5706548	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:5705579-5706739	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr11:5705984-5706539	HUVEC	blood vessel:	n/a	n/a
34	USF2	chr11:5705792-5706558	Hela-S3	cervix:	n/a	n/a
35	RFX5	chr11:5705758-5706569	GM12878	blood:	n/a	chr11:5706428-5706445
36	FOSL2	chr11:5705897-5706587	A549	lung:	n/a	chr11:5706370-5706378
37	HEY1	chr11:5706029-5706527	K562	blood:	n/a	n/a
38	JUND	chr11:5706042-5706587	A549	lung:	n/a	chr11:5706370-5706378
39	TEAD4	chr11:5705707-5706619	K562	blood:	n/a	n/a
40	ZNF143	chr11:5705698-5706549	GM12878	blood:	n/a	n/a
41	POLR2A	chr11:5705959-5706527	HCT-116	colon:	n/a	n/a
42	MAX	chr11:5705917-5706557	K562	blood:	n/a	n/a
43	POLR2A	chr11:5705598-5706615	HepG2	liver:	n/a	n/a
44	POLR2A	chr11:5704924-5706864	GM15510	blood:	n/a	n/a
45	TAF1	chr11:5705801-5706587	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr11:5705981-5706716	SK-N-SH	brain:	n/a	n/a
47	CTCF	chr11:5705321-5706844	A549	lung:	n/a	chr11:5705994-5706007
48	HCFC1	chr11:5705699-5706539	K562	blood:	n/a	n/a
49	STAT3	chr11:5705767-5706615	GM12878	blood:	n/a	chr11:5705896-5705908 chr11:5706124-5706131 chr11:5706270-5706278 chr11:5706322-5706333
50	TBL1XR1	chr11:5705812-5706661	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:5523660..5528079-chr11:5704615..5707879,4	K562	blood:
2	chr11:5706176..5707758-chr11:5710825..5713115,2	K562	blood:
3	11:5033143-5038367..11:5700314-5707362	K562	blood:
4	11:4801044-4820112..11:5700314-5707362	H1-hESC	embryonic stem cell:	embryo
5	11:4988858-5002113..11:5700314-5707362	Hela-S3	cervix:
6	chr11:5524818..5527723-chr11:5704615..5707499,2	K562	blood:

Variant related genes	Relation type
TRIM5	TF binding region
TRIM22	TF binding region
ENSG00000225003	Chromatin interaction
ENSG00000231070	Chromatin interaction
ENSG00000196565	Chromatin interaction
ENSG00000176951	Chromatin interaction
ENSG00000167355	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000213931	Chromatin interaction
ENSG00000224300	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11038702	0.83[EUR][1000 genomes]
rs12164821	0.81[ASN][1000 genomes]
rs12278842	0.94[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12285766	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12287199	0.94[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12799127	0.85[AMR][1000 genomes]
rs12799329	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12801311	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1498553	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1498555	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1814722	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2133256	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2343227	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2343229	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2880576	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3207178	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34506684	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34720081	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3802980	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4514451	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4564369	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4575305	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4992797	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4992798	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992799	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992801	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992802	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61363160	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6578674	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6578675	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6578676	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6578677	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67656732	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7122886	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7123417	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7127617	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7127767	0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7129909	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046068	chr11:5335943-6063742	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv896939	chr11:5497799-5809548	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
3	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1041568	chr11:5585716-5765688	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
5	nsv1053414	chr11:5612989-6030212	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic 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	50 gene(s)	inside rSNPs	diseases
6	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv553273	chr11:5639873-5871831	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers 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 target site	37 gene(s)	inside rSNPs	diseases
8	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
9	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
10	nsv896948	chr11:5701281-5719667	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3802981	DNHD1	cis	cerebellum	SCAN
rs3802981	OR51B4	cis	cerebellum	SCAN
rs3802981	OR52W1	cis	cerebellum	SCAN
rs3802981	CNGA4	cis	cerebellum	SCAN
rs3802981	OR52M1	cis	cerebellum	SCAN
rs3802981	OR52I2	cis	cerebellum	SCAN
rs3802981	OR52E6	cis	parietal	SCAN
rs3802981	SNORA23	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:5704600-5706600	Active TSS	Colonic Mucosa	Colon
2	chr11:5704600-5706800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:5704600-5706800	Active TSS	Stomach Smooth Muscle	stomach
4	chr11:5704800-5706600	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr11:5705000-5706600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr11:5705000-5706600	Active TSS	Fetal Intestine Small	intestine
7	chr11:5705000-5706600	Active TSS	Thymus	Thymus
8	chr11:5705000-5706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:5705000-5706800	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr11:5705200-5706600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:5705200-5706600	Active TSS	Liver	Liver
12	chr11:5705200-5706600	Active TSS	Brain Angular Gyrus	brain
13	chr11:5705200-5706600	Active TSS	Fetal Stomach	stomach
14	chr11:5705200-5706600	Active TSS	Small Intestine	intestine
15	chr11:5705200-5706600	Active TSS	A549	lung
16	chr11:5705200-5706800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:5705200-5706800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr11:5705200-5706800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr11:5705200-5706800	Active TSS	GM12878-XiMat	blood
20	chr11:5705400-5706600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr11:5705400-5706600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:5705400-5706600	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr11:5705400-5706600	Active TSS	Brain Hippocampus Middle	brain
24	chr11:5705400-5706600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:5705400-5706600	Active TSS	Brain Substantia Nigra	brain
26	chr11:5705400-5706600	ZNF genes & repeats	Fetal Brain Male	brain
27	chr11:5705400-5706600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr11:5705400-5706600	Active TSS	Psoas Muscle	Psoas
29	chr11:5705400-5706600	Active TSS	Right Atrium	heart
30	chr11:5705400-5706800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr11:5705400-5706800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr11:5705400-5706800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:5705400-5707400	Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr11:5705600-5706600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr11:5705600-5706800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr11:5705800-5706600	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr11:5705800-5706800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:5705800-5706800	Active TSS	Primary T cells from cord blood	blood
39	chr11:5706000-5706600	Active TSS	HSMMtube	muscle
40	chr11:5706200-5706600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr11:5706200-5706600	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr11:5706200-5706800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr11:5706200-5706800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:5706200-5706800	Flanking Active TSS	Dnd41	blood
45	chr11:5706200-5710000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:5706200-5711000	Weak transcription	Gastric	stomach
47	chr11:5706400-5706600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr11:5706400-5706600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr11:5706400-5706600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:5706400-5706600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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