Variant report

Variant	rs7938647
Chromosome Location	chr11:10061423-10061424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10840315	1.00[CHB][hapmap]
rs10840325	1.00[CHB][hapmap]
rs10840327	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs10840330	0.85[CEU][hapmap]
rs10840333	0.85[CEU][hapmap]
rs10840334	0.85[CEU][hapmap]
rs10840337	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840344	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840359	0.89[EUR][1000 genomes]
rs10840375	0.83[EUR][1000 genomes]
rs10840377	1.00[CEU][hapmap]
rs11042511	1.00[CHB][hapmap]
rs11042526	1.00[CHB][hapmap]
rs11042543	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.83[TSI][hapmap]
rs11042550	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11042556	1.00[CHB][hapmap]
rs11042559	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs11042561	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs11042571	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042578	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042579	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042580	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11042593	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042615	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11042618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042627	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11042632	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11042641	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11600251	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11600489	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11602465	0.82[EUR][1000 genomes]
rs11602515	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs11603291	1.00[CHD][hapmap]
rs11603440	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606561	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11607582	1.00[CHB][hapmap]
rs11607682	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11607703	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12360783	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12362060	0.95[CEU][hapmap]
rs12362938	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12364676	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417184	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12418212	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418619	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12419564	1.00[CHB][hapmap]
rs12419923	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12420122	0.81[EUR][1000 genomes]
rs12420734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12420950	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12421179	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421200	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421931	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12808226	1.00[CHB][hapmap]
rs1372807	0.91[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs1372808	0.80[EUR][1000 genomes]
rs1442737	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17270804	1.00[CHB][hapmap]
rs17271847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355675	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap]
rs17355924	1.00[CHB][hapmap]
rs17356792	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17359113	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1822291	0.81[EUR][1000 genomes]
rs1822292	0.95[CEU][hapmap];0.94[TSI][hapmap]
rs1867135	0.84[EUR][1000 genomes]
rs2197171	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2403227	0.86[CEU][hapmap]
rs2403229	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs2403292	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs28731164	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34683105	0.87[EUR][1000 genomes]
rs4271380	0.81[EUR][1000 genomes]
rs4281477	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4385889	0.81[EUR][1000 genomes]
rs4478985	0.87[EUR][1000 genomes]
rs4519084	0.81[EUR][1000 genomes]
rs4529876	0.88[EUR][1000 genomes]
rs4576815	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4625455	0.91[CEU][hapmap]
rs4909915	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs4909917	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4910075	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap]
rs4910080	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs4910081	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs4910084	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4910086	0.86[CEU][hapmap];0.80[TSI][hapmap]
rs4910095	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4910098	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55796222	0.81[EUR][1000 genomes]
rs56853694	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61877048	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61877049	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878582	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878587	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878622	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61878636	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114303	0.91[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs7115754	1.00[CHD][hapmap]
rs7123453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7123820	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7131445	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924875	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7928959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7931804	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935774	0.82[EUR][1000 genomes]
rs7935934	1.00[CEU][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7938491	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7938502	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938788	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs7945980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7946995	0.89[EUR][1000 genomes]
rs7947306	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7948215	0.83[EUR][1000 genomes]
rs7950447	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv553476	chr11:10024311-10117435	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7938647	SYT9	cis	cerebellum	SCAN
rs7938647	OR10A5	cis	cerebellum	SCAN
rs7938647	ZNF143	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10001400-10066200	Weak transcription	Pancreas	Pancrea
2	chr11:10030600-10065800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr11:10035200-10065800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr11:10036200-10062800	Weak transcription	Adipose Nuclei	Adipose
5	chr11:10040400-10065800	Weak transcription	HSMM	muscle
6	chr11:10042200-10064400	Weak transcription	Fetal Intestine Small	intestine
7	chr11:10042200-10066000	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:10042200-10066000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:10042200-10066200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:10042600-10066000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:10043400-10065600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:10043800-10063800	Weak transcription	Primary T cells from cord blood	blood
13	chr11:10043800-10065400	Weak transcription	A549	lung
14	chr11:10043800-10065600	Weak transcription	HepG2	liver
15	chr11:10046400-10065800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:10046400-10065800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:10048600-10064600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:10049200-10063200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:10049200-10065000	Weak transcription	Dnd41	blood
20	chr11:10049400-10065600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:10049800-10065000	Weak transcription	Fetal Intestine Large	intestine
22	chr11:10049800-10065600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr11:10049800-10066000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:10049800-10066000	Weak transcription	Fetal Kidney	kidney
25	chr11:10050200-10066000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:10050200-10066800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:10050600-10064200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr11:10050600-10065000	Weak transcription	Placenta	Placenta
29	chr11:10051400-10062200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr11:10051400-10063400	Weak transcription	Liver	Liver
31	chr11:10052000-10062600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr11:10054200-10063200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:10056000-10063200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr11:10056200-10063800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:10056200-10066000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:10057600-10063800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr11:10058400-10061600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr11:10058600-10061600	Enhancers	NHDF-Ad	bronchial
39	chr11:10059200-10061800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:10059600-10061800	Enhancers	Hela-S3	cervix
41	chr11:10060000-10061600	Enhancers	Osteobl	bone
42	chr11:10060200-10062800	Weak transcription	Fetal Lung	lung
43	chr11:10060600-10063800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr11:10060600-10065400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr11:10061000-10061800	Enhancers	NHLF	lung
46	chr11:10061000-10063600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:10061000-10063800	Enhancers	Primary hematopoietic stem cells	blood
48	chr11:10061200-10061800	Enhancers	HUVEC	blood vessel
49	chr11:10061200-10062000	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr11:10061200-10064200	Weak transcription	Muscle Satellite Cultured Cells	--

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