Variant report

Variant	rs10835262
Chromosome Location	chr11:3916506-3916507
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	EBF1	chr11:3916455-3916513	GM12878	blood:	n/a	n/a
2	POLR2A	chr11:3916354-3916508	GM12878	blood:	n/a	n/a
3	NR3C1	chr11:3916235-3916593	A549	lung:	n/a	chr11:3916381-3916407 chr11:3916383-3916404 chr11:3916381-3916407 chr11:3916386-3916402 chr11:3916387-3916401 chr11:3916386-3916402 chr11:3916386-3916402 chr11:3916381-3916407
4	NR3C1	chr11:3916261-3916631	A549	lung:	n/a	chr11:3916381-3916407 chr11:3916383-3916404 chr11:3916381-3916407 chr11:3916386-3916402 chr11:3916387-3916401 chr11:3916386-3916402 chr11:3916386-3916402 chr11:3916381-3916407
5	NR3C1	chr11:3916217-3916526	A549	lung:	n/a	chr11:3916381-3916407 chr11:3916383-3916404 chr11:3916381-3916407 chr11:3916386-3916402 chr11:3916387-3916401 chr11:3916386-3916402 chr11:3916386-3916402 chr11:3916381-3916407
6	FOXA2	chr11:3916159-3916599	A549	lung:	n/a	n/a
7	NR3C1	chr11:3916091-3916649	A549	lung:	n/a	chr11:3916381-3916407 chr11:3916383-3916404 chr11:3916381-3916407 chr11:3916386-3916402 chr11:3916387-3916401 chr11:3916386-3916402 chr11:3916386-3916402 chr11:3916381-3916407
8	NR3C1	chr11:3916184-3916642	A549	lung:	n/a	chr11:3916381-3916407 chr11:3916383-3916404 chr11:3916381-3916407 chr11:3916386-3916402 chr11:3916387-3916401 chr11:3916386-3916402 chr11:3916386-3916402 chr11:3916381-3916407
9	ESRRA	chr11:3914109-3916888	GM12878	blood:	n/a	chr11:3914726-3914736 chr11:3916295-3916307 chr11:3914722-3914738 chr11:3914726-3914738 chr11:3915715-3915725 chr11:3916290-3916306 chr11:3914726-3914736 chr11:3915715-3915727 chr11:3916409-3916422
10	NR3C1	chr11:3916167-3916583	A549	lung:	n/a	chr11:3916381-3916407 chr11:3916383-3916404 chr11:3916381-3916407 chr11:3916386-3916402 chr11:3916387-3916401 chr11:3916386-3916402 chr11:3916386-3916402 chr11:3916381-3916407
11	FOXA1	chr11:3916228-3916657	A549	lung:	n/a	n/a
12	FOXA2	chr11:3916314-3916673	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:3906966..3908700-chr11:3915127..3916837,2	MCF-7	breast:
2	chr11:3912079..3914672-chr11:3914828..3918304,3	K562	blood:

Variant related genes	Relation type
ENSG00000230593	TF binding region
ENSG00000230593	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10160254	0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10160331	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10160415	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10160703	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10160753	0.96[ASN][1000 genomes]
rs10767679	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10767680	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10767681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10767684	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10767685	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10835217	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10835226	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835231	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835232	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10835236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835238	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835245	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835246	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835247	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10835248	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10835249	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10835250	0.96[ASN][1000 genomes]
rs10835252	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10835256	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10835261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835270	0.94[MEX][hapmap];0.86[TSI][hapmap]
rs11030122	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11030176	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11030209	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11030211	0.85[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs12275981	0.88[ASN][1000 genomes]
rs1869084	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs1869085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1964492	0.81[ASN][1000 genomes]
rs4414209	0.95[CEU][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4598668	0.85[JPT][hapmap]
rs4622250	1.00[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs4910584	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7111609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113148	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7118295	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120336	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131469	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7932404	0.85[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking 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 miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1051580	chr11:3856201-3924216	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1043265	chr11:3856201-3926407	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
10	nsv869701	chr11:3879297-3973762	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	nsv1051904	chr11:3903226-3939186	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv1050077	chr11:3903226-3940726	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv1043039	chr11:3903226-3955159	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10835262	STIM1	cis	Thyroid	GTEx
rs10835262	CD81	cis	parietal	SCAN
rs10835262	OR51G2	cis	parietal	SCAN
rs10835262	TRIM21	cis	cerebellum	SCAN
rs10835262	IFITM3	cis	parietal	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3899200-3926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:3902400-3923800	Weak transcription	Gastric	stomach
3	chr11:3907400-3923600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr11:3907600-3922600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:3911200-3916800	Enhancers	Dnd41	blood
6	chr11:3912600-3916800	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr11:3913000-3916800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr11:3913000-3916800	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr11:3913000-3916800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr11:3913400-3918800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr11:3913600-3916600	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr11:3913800-3917000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr11:3913800-3917800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr11:3914000-3916600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:3914000-3916600	Enhancers	Placenta	Placenta
16	chr11:3914000-3918000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr11:3914200-3916600	Enhancers	Primary hematopoietic stem cells	blood
18	chr11:3914200-3916600	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr11:3914200-3917000	Enhancers	Liver	Liver
20	chr11:3914400-3916600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr11:3914400-3916600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr11:3914400-3916800	Enhancers	A549	lung
23	chr11:3914400-3916800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr11:3914600-3916600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr11:3914600-3916600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:3914600-3916600	Enhancers	Fetal Thymus	thymus
27	chr11:3914600-3916600	Enhancers	Pancreas	Pancrea
28	chr11:3914600-3916600	Enhancers	Rectal Mucosa Donor 29	rectum
29	chr11:3914600-3916600	Enhancers	NHDF-Ad	bronchial
30	chr11:3914600-3916600	Enhancers	Osteobl	bone
31	chr11:3914800-3916600	Enhancers	Primary T cells fromperipheralblood	blood
32	chr11:3914800-3916800	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr11:3915000-3916600	Enhancers	Adipose Nuclei	Adipose
34	chr11:3915000-3916600	Enhancers	Fetal Muscle Leg	muscle
35	chr11:3915200-3916600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr11:3915200-3916600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr11:3915200-3916600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr11:3915200-3916600	Enhancers	Esophagus	oesophagus
39	chr11:3915200-3916600	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr11:3915200-3916600	Enhancers	Right Atrium	heart
41	chr11:3915200-3916600	Enhancers	Stomach Mucosa	stomach
42	chr11:3915200-3916600	Enhancers	HUVEC	blood vessel
43	chr11:3915200-3916800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:3915200-3916800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr11:3915200-3916800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:3915200-3916800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr11:3915200-3916800	Enhancers	Right Ventricle	heart
48	chr11:3915400-3916600	Enhancers	Lung	lung
49	chr11:3915400-3918600	Enhancers	Primary B cells from peripheral blood	blood
50	chr11:3915600-3916600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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