Variant report

Variant	rs10835261
Chromosome Location	chr11:3916501-3916502
allele	A/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	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: 51 )
Associated
traits (count: 1 )

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

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	0.96[ASN][1000 genomes]
rs10160753	0.96[ASN][1000 genomes]
rs10767679	0.96[ASN][1000 genomes]
rs10767680	0.96[ASN][1000 genomes]
rs10767681	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	0.96[ASN][1000 genomes]
rs10835236	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	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	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]
rs10835262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030122	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]
rs12275981	0.88[ASN][1000 genomes]
rs1869085	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1964492	0.81[ASN][1000 genomes]
rs4414209	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4910584	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7111609	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
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	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]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10835261	STIM1	cis	Thyroid	GTEx

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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