Variant report

Variant	rs12611958
Chromosome Location	chr2:11576413-11576414
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10186511	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10929736	0.95[CEU][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10929737	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10929739	0.95[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10929740	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10929741	0.84[ASN][1000 genomes]
rs10929742	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674593	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11680919	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11682602	0.95[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11685543	0.89[ASN][1000 genomes]
rs11686138	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687178	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11687681	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691211	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11693023	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11694857	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472962	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612948	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12613503	0.95[CEU][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12614218	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12615317	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617534	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12988106	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12990560	0.91[CEU][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs12995996	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13007909	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34079430	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34514099	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35053846	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35306821	0.99[ASN][1000 genomes]
rs35423645	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35727311	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818376	0.89[ASN][1000 genomes]
rs3922995	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4292073	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4335920	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4491705	0.83[ASN][1000 genomes]
rs4553788	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4588159	0.91[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57197575	0.85[EUR][1000 genomes]
rs61016299	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432192	0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs6432193	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432195	0.83[ASN][1000 genomes]
rs6432196	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6708001	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6708015	0.95[CEU][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6729114	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735687	0.81[EUR][1000 genomes]
rs6735707	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6736199	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6750266	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6750482	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6750499	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6751915	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7425786	0.99[ASN][1000 genomes]
rs7556984	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7584175	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595697	0.87[EUR][1000 genomes]
rs9789694	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12611958	ITGB1BP1	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11546600-11584200	Weak transcription	Pancreas	Pancrea
2	chr2:11560400-11584000	Weak transcription	Aorta	Aorta
3	chr2:11560600-11576800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:11561200-11579200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:11562800-11582400	Weak transcription	Left Ventricle	heart
6	chr2:11563000-11583800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:11563000-11586800	Weak transcription	Psoas Muscle	Psoas
8	chr2:11563400-11581600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:11564200-11580000	Weak transcription	Ovary	ovary
10	chr2:11565600-11578600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:11566600-11577800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:11567800-11577000	Weak transcription	HSMM	muscle
13	chr2:11569000-11578200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:11569600-11581800	Weak transcription	HepG2	liver
15	chr2:11570800-11577800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:11571200-11582600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:11571200-11582800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:11571400-11580000	Weak transcription	HSMMtube	muscle
19	chr2:11571400-11581800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:11571600-11580000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:11571800-11577400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:11571800-11581600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:11572400-11580000	Weak transcription	Gastric	stomach
24	chr2:11572400-11583800	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:11572600-11578400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:11572600-11588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr2:11572800-11578000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:11573000-11577400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:11573200-11580000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:11573400-11577600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:11573800-11582000	Strong transcription	A549	lung
32	chr2:11574000-11578200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr2:11574000-11581800	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:11574000-11582400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:11574200-11577000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:11574200-11578600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:11574200-11583000	Weak transcription	K562	blood
38	chr2:11574400-11576800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:11574400-11577600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:11574400-11578000	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:11574600-11581800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:11574800-11580000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:11575000-11578600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr2:11575000-11578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr2:11575000-11584800	Weak transcription	Esophagus	oesophagus
46	chr2:11575200-11578800	Weak transcription	Fetal Intestine Small	intestine
47	chr2:11575200-11581800	Weak transcription	Fetal Muscle Trunk	muscle
48	chr2:11575200-11584000	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:11575400-11578200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:11575400-11583800	Weak transcription	Osteobl	bone

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