Variant report

Variant	rs3802980
Chromosome Location	chr11:5706311-5706312
allele	A/G
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	POLR2A	chr11:5705819-5706508	GM12892	blood:	n/a	n/a
3	YY1	chr11:5705905-5706440	GM12892	blood:	n/a	n/a
4	EGR1	chr11:5705840-5706393	K562	blood:	n/a	chr11:5706060-5706073 chr11:5706059-5706073 chr11:5706057-5706071 chr11:5706060-5706073 chr11:5706059-5706074 chr11:5706061-5706070 chr11:5706060-5706073 chr11:5706055-5706077 chr11:5706061-5706071 chr11:5706060-5706073
5	CTCF	chr11:5705739-5706470	GM12878	blood:	n/a	chr11:5705994-5706007
6	PML	chr11:5705922-5706501	GM12878	blood:	n/a	chr11:5706283-5706291
7	POLR2A	chr11:5706183-5706507	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUND	chr11:5705838-5706660	K562	blood:	n/a	chr11:5706370-5706378
9	TEAD4	chr11:5705824-5706499	K562	blood:	n/a	n/a
10	POLR2A	chr11:5705888-5706399	H1-hESC	embryonic stem cell:	n/a	n/a
11	IRF4	chr11:5705833-5706326	GM12878	blood:	n/a	n/a
12	NFYB	chr11:5706041-5706614	Hela-S3	cervix:	n/a	chr11:5706337-5706352
13	POLR2A	chr11:5705969-5706480	ECC-1	luminal epithelium:	n/a	n/a
14	CREB1	chr11:5705845-5706640	HepG2	liver:	n/a	n/a
15	CUX1	chr11:5705816-5706478	K562	blood:	n/a	n/a
16	TAF1	chr11:5706091-5706408	GM12891	blood:	n/a	n/a
17	POLR2A	chr11:5705887-5706590	U87	brain:	n/a	n/a
18	POLR2A	chr11:5705798-5706635	GM12892	blood:	n/a	n/a
19	RELA	chr11:5705574-5706758	GM10847	blood:	n/a	n/a
20	RCOR1	chr11:5705902-5706392	K562	blood:	n/a	n/a
21	FOXM1	chr11:5705761-5706600	GM12878	blood:	n/a	chr11:5706457-5706465
22	POLR2A	chr11:5705807-5706653	HUVEC	blood vessel:	n/a	n/a
23	MXI1	chr11:5705977-5706334	K562	blood:	n/a	n/a
24	POLR2A	chr11:5705881-5706596	U87	brain:	n/a	n/a
25	TBL1XR1	chr11:5705794-5706617	GM12878	blood:	n/a	n/a
26	GTF2F1	chr11:5705621-5706610	Hela-S3	cervix:	n/a	n/a
27	RCOR1	chr11:5705992-5706453	HepG2	liver:	n/a	n/a
28	IKZF1	chr11:5705921-5706569	GM12878	blood:	n/a	chr11:5706448-5706460
29	GATA2	chr11:5705806-5706527	HUVEC	blood vessel:	n/a	chr11:5706018-5706025
30	POLR2A	chr11:5705886-5706509	K562	blood:	n/a	n/a
31	MAFK	chr11:5705959-5706515	IMR90	lung:	n/a	n/a
32	POU2F2	chr11:5705868-5706552	GM12891	blood:	n/a	n/a
33	CREB1	chr11:5705955-5706589	HepG2	liver:	n/a	n/a
34	JUND	chr11:5705917-5706695	SK-N-SH	brain:	n/a	chr11:5706370-5706378
35	EBF1	chr11:5705766-5706649	GM12878	blood:	n/a	n/a
36	CREB1	chr11:5705988-5706579	H1-hESC	embryonic stem cell:	n/a	n/a
37	REST	chr11:5706199-5706430	K562	blood:	n/a	n/a
38	JUN	chr11:5705823-5706646	K562	blood:	n/a	chr11:5706370-5706378
39	RCOR1	chr11:5705662-5706520	GM12878	blood:	n/a	n/a
40	MAX	chr11:5705849-5706678	SK-N-SH	brain:	n/a	n/a
41	TAF1	chr11:5706117-5706358	SK-N-SH	brain:	n/a	n/a
42	UBTF	chr11:5705604-5706425	K562	blood:	n/a	n/a
43	TBL1XR1	chr11:5705652-5706492	K562	blood:	n/a	n/a
44	NFIC	chr11:5705792-5706452	GM12878	blood:	n/a	n/a
45	E2F4	chr11:5705935-5706478	GM12878	blood:	n/a	chr11:5705978-5705987
46	NRF1	chr11:5705836-5706441	GM12878	blood:	n/a	n/a
47	SP1	chr11:5705754-5706593	A549	lung:	n/a	chr11:5706376-5706388 chr11:5706376-5706388 chr11:5706059-5706068
48	IRF3	chr11:5705889-5706507	Hela-S3	cervix:	n/a	chr11:5706322-5706336 chr11:5706374-5706388 chr11:5706322-5706332 chr11:5706318-5706332 chr11:5706319-5706336 chr11:5706320-5706333 chr11:5706322-5706333 chr11:5706082-5706094 chr11:5706321-5706338
49	TBP	chr11:5706009-5706545	H1-hESC	embryonic stem cell:	n/a	n/a
50	SPI1	chr11:5705811-5706528	HL-60	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
TRIM22	TF binding region
TRIM5	TF binding region
ENSG00000224300	Chromatin interaction
ENSG00000231070	Chromatin interaction
ENSG00000132274	Chromatin interaction
ENSG00000176951	Chromatin interaction
ENSG00000213931	Chromatin interaction
ENSG00000167355	Chromatin interaction
ENSG00000196565	Chromatin interaction
ENSG00000225003	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11038702	0.83[EUR][1000 genomes]
rs12278842	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12285766	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12287199	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12799127	0.85[AMR][1000 genomes]
rs12799329	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12801311	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1498553	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1498555	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1814722	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2133256	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2343227	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2343229	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2880576	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3207178	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34506684	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34720081	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3802981	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];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4564369	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4575305	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4992797	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992798	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992799	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992801	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4992802	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61363160	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6578674	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6578675	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6578676	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6578677	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67656732	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7122886	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7123417	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7127617	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7127767	1.00[CHB][hapmap];0.95[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];0.96[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
rs3802980	OR52E6	cis	parietal	SCAN
rs3802980	OR52W1	cis	cerebellum	SCAN
rs3802980	DNHD1	cis	cerebellum	SCAN
rs3802980	CNGA4	cis	cerebellum	SCAN
rs3802980	OR51B4	cis	cerebellum	SCAN
rs3802980	OR52M1	cis	cerebellum	SCAN
rs3802980	SNORA23	cis	cerebellum	SCAN
rs3802980	OR52I2	cis	cerebellum	SCAN

Chromatin state (count:126 , 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	chr11:5705000-5706400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr11:5705000-5706400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:5705000-5706400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:5705000-5706400	Active TSS	Colon Smooth Muscle	Colon
9	chr11:5705000-5706400	Active TSS	Fetal Lung	lung
10	chr11:5705000-5706400	Active TSS	Pancreas	Pancrea
11	chr11:5705000-5706400	Active TSS	NHLF	lung
12	chr11:5705000-5706600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr11:5705000-5706600	Active TSS	Fetal Intestine Small	intestine
14	chr11:5705000-5706600	Active TSS	Thymus	Thymus
15	chr11:5705000-5706800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr11:5705000-5706800	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr11:5705200-5706400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:5705200-5706400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:5705200-5706400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr11:5705200-5706400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:5705200-5706400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:5705200-5706400	Active TSS	Fetal Intestine Large	intestine
23	chr11:5705200-5706400	Active TSS	Lung	lung
24	chr11:5705200-5706400	Active TSS	Right Ventricle	heart
25	chr11:5705200-5706400	Active TSS	HSMM	muscle
26	chr11:5705200-5706600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:5705200-5706600	Active TSS	Liver	Liver
28	chr11:5705200-5706600	Active TSS	Brain Angular Gyrus	brain
29	chr11:5705200-5706600	Active TSS	Fetal Stomach	stomach
30	chr11:5705200-5706600	Active TSS	Small Intestine	intestine
31	chr11:5705200-5706600	Active TSS	A549	lung
32	chr11:5705200-5706800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:5705200-5706800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr11:5705200-5706800	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr11:5705200-5706800	Active TSS	GM12878-XiMat	blood
36	chr11:5705400-5706400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr11:5705400-5706400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:5705400-5706400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr11:5705400-5706400	Active TSS	iPS-18 Cell Line	embryonic stem cell
40	chr11:5705400-5706400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:5705400-5706400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr11:5705400-5706400	Active TSS	Brain Anterior Caudate	brain
43	chr11:5705400-5706400	Active TSS	Brain Cingulate Gyrus	brain
44	chr11:5705400-5706400	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr11:5705400-5706400	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr11:5705400-5706400	Flanking Active TSS	Placenta	Placenta
47	chr11:5705400-5706400	Active TSS	Left Ventricle	heart
48	chr11:5705400-5706400	Active TSS	Ovary	ovary
49	chr11:5705400-5706400	Active TSS	HepG2	liver
50	chr11:5705400-5706400	Active TSS	NHDF-Ad	bronchial

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