Variant report

Variant	rs1150955
Chromosome Location	chr12:31684779-31684780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs1012154	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10743757	0.81[CHB][hapmap]
rs10771832	0.86[CHB][hapmap]
rs10843947	0.86[CHB][hapmap]
rs11051418	0.85[CHB][hapmap]
rs11051441	0.81[CHB][hapmap]
rs11051456	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150942	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150943	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150945	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150950	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1150953	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1150954	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150963	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615961	0.86[CHB][hapmap]
rs1259233	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259235	0.95[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1259241	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259352	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1259353	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259354	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259356	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259359	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1259389	0.85[ASN][1000 genomes]
rs1259395	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259405	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1259422	0.92[AFR][1000 genomes]
rs1259426	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1259428	0.81[CHB][hapmap]
rs1259430	0.90[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259432	0.86[AMR][1000 genomes]
rs1259435	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259437	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259438	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1262390	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1271128	0.86[AMR][1000 genomes]
rs1271663	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1272773	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469673	0.86[CHB][hapmap]
rs1542536	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1677154	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1677186	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677187	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1677189	0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1677217	0.83[EUR][1000 genomes]
rs1716194	0.82[ASN][1000 genomes]
rs1716216	1.00[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2061761	0.95[CEU][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2116704	0.86[CHB][hapmap]
rs2374190	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap]
rs2568884	0.93[CHB][hapmap]
rs2568885	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2568887	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2568888	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2568894	0.84[AMR][1000 genomes]
rs2568902	0.90[AMR][1000 genomes]
rs2604052	0.91[ASN][1000 genomes]
rs2617178	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2617191	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617200	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2682671	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682674	0.86[ASN][1000 genomes]
rs2682677	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682679	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682680	0.89[ASN][1000 genomes]
rs2682686	0.82[EUR][1000 genomes]
rs2682695	0.87[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682697	0.84[CHB][hapmap]
rs3850965	0.81[CHB][hapmap]
rs3898368	0.86[CHB][hapmap]
rs4312145	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4482118	0.81[CHB][hapmap]
rs4931501	0.81[CHB][hapmap]
rs4931507	0.81[CHB][hapmap]
rs6487992	0.81[CHB][hapmap]
rs708200	0.89[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs708209	0.86[CHB][hapmap]
rs708212	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs708215	0.93[AMR][1000 genomes]
rs708217	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes]
rs7133082	0.81[CHB][hapmap]
rs7135856	0.81[CHB][hapmap]
rs7294574	0.86[CHB][hapmap]
rs7302698	0.86[CHB][hapmap]
rs7307616	0.81[CHB][hapmap]
rs7313118	0.81[CHB][hapmap]
rs792871	0.84[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs792875	0.93[AMR][1000 genomes]
rs793148	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793149	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793150	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793158	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793161	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes]
rs793171	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs793173	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793174	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793175	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793176	0.92[CHB][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs793177	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793186	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793191	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs7954595	0.81[CHB][hapmap]
rs7959877	0.86[CHB][hapmap]
rs7962896	0.86[CHB][hapmap]
rs7974437	0.81[CHB][hapmap]
rs7975761	0.86[CHB][hapmap]
rs7976644	0.86[CHB][hapmap]
rs899159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs976874	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1150955	PTHLH	cis	cerebellum	SCAN
rs1150955	DENND5B	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
2	chr12:31673000-31685200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:31673400-31688400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:31675600-31689000	Weak transcription	Small Intestine	intestine
5	chr12:31676000-31685800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:31678000-31686400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr12:31678200-31686400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:31679000-31688800	Weak transcription	Psoas Muscle	Psoas
9	chr12:31679000-31691400	Weak transcription	Fetal Intestine Large	intestine
10	chr12:31679400-31687600	Weak transcription	Primary B cells from cord blood	blood
11	chr12:31679600-31686400	Weak transcription	Fetal Intestine Small	intestine
12	chr12:31679800-31686000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:31679800-31692000	Weak transcription	GM12878-XiMat	blood
14	chr12:31680200-31686400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:31680400-31684800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:31680400-31685200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:31680400-31685800	Weak transcription	Adipose Nuclei	Adipose
18	chr12:31680400-31685800	Weak transcription	HepG2	liver
19	chr12:31680400-31686400	Weak transcription	Fetal Heart	heart
20	chr12:31680400-31686400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:31680600-31685200	Weak transcription	Right Ventricle	heart
22	chr12:31680600-31687800	Weak transcription	Left Ventricle	heart
23	chr12:31681200-31686600	Enhancers	A549	lung
24	chr12:31681200-31691000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:31681200-31691600	Weak transcription	Fetal Muscle Leg	muscle
26	chr12:31681400-31685800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:31681400-31686600	Weak transcription	Brain Anterior Caudate	brain
28	chr12:31683600-31684800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:31683600-31685200	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr12:31683600-31685400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr12:31683600-31687000	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr12:31684000-31685400	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr12:31684000-31685800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:31684000-31686400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr12:31684200-31685200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:31684200-31685400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:31684200-31686600	Enhancers	Ovary	ovary
38	chr12:31684400-31685600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:31684400-31687200	Enhancers	Osteobl	bone
40	chr12:31684600-31684800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:31684600-31685000	Enhancers	Fetal Kidney	kidney
42	chr12:31684600-31685400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr12:31684600-31685400	Enhancers	Aorta	Aorta
44	chr12:31684600-31685600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr12:31684600-31686000	Enhancers	HSMM	muscle
46	chr12:31684600-31686200	Enhancers	Primary B cells from peripheral blood	blood
47	chr12:31684600-31687000	Enhancers	Hela-S3	cervix

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