Variant report

Variant	rs2959068
Chromosome Location	chr11:4077048-4077049
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	POLR2A	chr11:4076550-4077201	K562	blood:	n/a	n/a
2	POLR2A	chr11:4076646-4077284	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
STIM1	TF binding region

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10742189	0.82[GIH][hapmap]
rs10742223	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10767807	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10835613	0.88[CHD][hapmap]
rs11030841	0.85[MKK][hapmap];0.80[YRI][hapmap]
rs11030853	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11030907	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11030976	0.88[CHD][hapmap]
rs11604649	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12364664	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12419208	0.81[ASN][1000 genomes]
rs12799265	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12803023	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1372804	0.80[MEX][hapmap]
rs1372805	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1662172	0.82[CHD][hapmap];0.87[MEX][hapmap]
rs2304891	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412344	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920139	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2920144	0.93[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2920145	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2923944	0.86[ASW][hapmap]
rs2923948	0.82[GIH][hapmap]
rs2923953	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2923956	0.93[ASW][hapmap];0.89[GIH][hapmap];0.87[MKK][hapmap]
rs2958714	0.86[ASW][hapmap];0.93[GIH][hapmap];0.85[MKK][hapmap]
rs2959066	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2959074	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959081	0.93[ASW][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.87[MKK][hapmap];0.80[YRI][hapmap]
rs7102508	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110060	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7116520	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7124301	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs725518	0.88[CHD][hapmap]
rs725519	0.88[CHD][hapmap]
rs747883	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7933164	0.90[MKK][hapmap];0.80[YRI][hapmap]
rs7945639	0.81[MKK][hapmap]
rs9704047	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv896896	chr11:4010409-4185595	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1042719	chr11:4017541-4101609	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2758253	chr11:4055945-4510188	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv2759797	chr11:4055945-4510188	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
5	nsv428248	chr11:4055945-4510188	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2959068	OR52I2	cis	parietal	SCAN
rs2959068	OR51T1	cis	parietal	SCAN
rs2959068	KRTAP5-4	cis	cerebellum	SCAN
rs2959068	RRM1	cis	cerebellum	SCAN
rs2959068	TRIM21	cis	cerebellum	SCAN
rs2959068	POLR2L	cis	cerebellum	SCAN
rs2959068	ANO9	cis	parietal	SCAN
rs2959068	RRM1	cis	Artery Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4047800-4077400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:4048000-4077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr11:4048600-4077800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:4051000-4080400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:4062000-4080400	Weak transcription	Spleen	Spleen
6	chr11:4066000-4079200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:4066200-4078400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:4066200-4079000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:4066200-4079200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:4066200-4104200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:4066400-4077400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:4066400-4077400	Weak transcription	Esophagus	oesophagus
13	chr11:4066400-4077600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:4066400-4107800	Weak transcription	Small Intestine	intestine
15	chr11:4066600-4077600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr11:4066600-4077600	Weak transcription	Left Ventricle	heart
17	chr11:4066600-4078400	Weak transcription	NHDF-Ad	bronchial
18	chr11:4066600-4078600	Weak transcription	K562	blood
19	chr11:4066600-4078600	Weak transcription	Osteobl	bone
20	chr11:4066600-4080200	Weak transcription	Right Ventricle	heart
21	chr11:4066600-4080400	Weak transcription	Fetal Lung	lung
22	chr11:4066600-4080400	Weak transcription	Gastric	stomach
23	chr11:4066600-4085800	Weak transcription	Pancreas	Pancrea
24	chr11:4066800-4078400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:4067000-4079200	Weak transcription	Colon Smooth Muscle	Colon
26	chr11:4067000-4087400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:4067800-4079200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:4067800-4080400	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:4067800-4080600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:4067800-4093200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:4068000-4077600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr11:4068000-4079000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr11:4068000-4079200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr11:4068000-4079400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:4068000-4080200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:4068000-4080200	Weak transcription	Psoas Muscle	Psoas
37	chr11:4068200-4077800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr11:4068200-4078400	Weak transcription	NHEK	skin
39	chr11:4068200-4079000	Weak transcription	HUVEC	blood vessel
40	chr11:4068600-4078600	Weak transcription	HMEC	breast
41	chr11:4068800-4078200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:4070800-4108600	Weak transcription	HSMM	muscle
43	chr11:4071000-4083600	Weak transcription	Fetal Brain Male	brain
44	chr11:4071600-4078200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr11:4071600-4080400	Weak transcription	Aorta	Aorta
46	chr11:4071800-4080600	Weak transcription	Colonic Mucosa	Colon
47	chr11:4073000-4093200	Weak transcription	Fetal Intestine Small	intestine
48	chr11:4075800-4077600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr11:4075800-4078400	Strong transcription	Primary B cells from cord blood	blood
50	chr11:4075800-4078600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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