Variant report

Variant	rs2967484
Chromosome Location	chr19:36808351-36808352
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10402043	0.82[CHB][hapmap]
rs10404574	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10409091	0.90[CHB][hapmap]
rs10414054	0.83[ASN][1000 genomes]
rs10418510	1.00[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10420071	0.86[ASW][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.86[LWK][hapmap];0.88[MKK][hapmap]
rs10420610	0.84[ASN][1000 genomes]
rs10439091	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12459465	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12971694	0.83[ASN][1000 genomes]
rs12976881	0.85[ASN][1000 genomes]
rs12986029	0.87[AMR][1000 genomes]
rs2070132	0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs2271844	1.00[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs2287897	0.90[CHB][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2287898	0.90[CHB][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2385799	0.86[ASN][1000 genomes]
rs2385800	0.86[ASN][1000 genomes]
rs2385801	1.00[ASW][hapmap];0.83[CEU][hapmap];0.82[CHD][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs2385803	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2385804	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs2385805	0.85[ASN][1000 genomes]
rs2432039	0.95[CHB][hapmap]
rs2432045	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2432049	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2432054	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2438514	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs2438517	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs2918349	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945945	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945949	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945950	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945951	0.85[ASN][1000 genomes]
rs2945957	0.85[ASN][1000 genomes]
rs2945961	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2945963	0.85[ASN][1000 genomes]
rs2945971	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945972	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945985	1.00[ASW][hapmap];0.83[CEU][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.83[YRI][hapmap]
rs2945992	0.84[ASN][1000 genomes]
rs2945993	1.00[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2945995	0.86[ASN][1000 genomes]
rs2967493	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967496	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967501	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967504	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2967506	0.87[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs2967509	0.87[ASN][1000 genomes]
rs2967510	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967512	0.86[ASN][1000 genomes]
rs2967515	0.85[ASN][1000 genomes]
rs2967517	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2967518	1.00[ASW][hapmap];0.82[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2967521	0.93[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs2967523	0.83[ASN][1000 genomes]
rs2967524	0.83[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[ASN][1000 genomes]
rs2967526	0.83[CEU][hapmap]
rs2972632	0.90[ASN][1000 genomes]
rs2972633	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4239585	0.95[CHB][hapmap]
rs4806321	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5021030	0.87[ASN][1000 genomes]
rs62112565	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6417185	0.85[ASN][1000 genomes]
rs6510541	0.85[ASN][1000 genomes]
rs6510542	0.83[ASN][1000 genomes]
rs7246106	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs7251979	0.84[ASN][1000 genomes]
rs7255260	0.87[ASN][1000 genomes]
rs7255403	0.87[ASN][1000 genomes]
rs8102020	0.90[CHB][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap]
rs8106095	0.89[ASN][1000 genomes]
rs8109320	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8109333	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8112312	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8182628	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv9715	chr19:36729688-36811749	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1063208	chr19:36743461-36847486	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv960831	chr19:36744378-36813769	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1061054	chr19:36751703-36847486	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1055260	chr19:36752221-36847486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1056850	chr19:36752663-36847486	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1064983	chr19:36752663-36847625	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1057579	chr19:36752663-36847822	Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1825146	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1837043	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv2763143	chr19:36805705-36847498	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1059568	chr19:36806475-36847864	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
16	esv1823621	chr19:36807288-36845863	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2967484	LOC284412	N/A	lymphoblastoid	RTeQTL
rs2967484	LINC00665	cis	Nerve Tibial	GTEx
rs2967484	ITPKC	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36799400-36816400	Weak transcription	Primary T cells from cord blood	blood
2	chr19:36799800-36809600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr19:36800400-36810000	Weak transcription	Placenta	Placenta
4	chr19:36800600-36810400	Weak transcription	Esophagus	oesophagus
5	chr19:36800600-36811200	Weak transcription	Pancreas	Pancrea
6	chr19:36800600-36816400	Weak transcription	Ovary	ovary
7	chr19:36800600-36816600	Weak transcription	Spleen	Spleen
8	chr19:36800800-36810000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:36800800-36816400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr19:36800800-36822000	Weak transcription	Psoas Muscle	Psoas
11	chr19:36801000-36810200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:36801000-36816400	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:36801200-36810200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:36801200-36810400	Weak transcription	Brain Germinal Matrix	brain
15	chr19:36801200-36814400	Weak transcription	Primary B cells from cord blood	blood
16	chr19:36801200-36816000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr19:36801200-36816200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:36801200-36816400	Weak transcription	Primary B cells from peripheral blood	blood
19	chr19:36801200-36816400	Weak transcription	Adipose Nuclei	Adipose
20	chr19:36801200-36816600	Weak transcription	Right Ventricle	heart
21	chr19:36801200-36817000	Weak transcription	Brain Anterior Caudate	brain
22	chr19:36801200-36817000	Weak transcription	Fetal Kidney	kidney
23	chr19:36801200-36817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:36801600-36809800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:36802200-36815800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr19:36802800-36816400	Weak transcription	Brain Hippocampus Middle	brain
27	chr19:36804000-36811600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:36804000-36820600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:36804200-36811200	Weak transcription	Fetal Lung	lung
30	chr19:36804600-36808600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:36804800-36820800	Weak transcription	Brain Angular Gyrus	brain
32	chr19:36805000-36811000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:36805000-36816600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:36805200-36816400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:36805400-36822000	Weak transcription	HSMMtube	muscle
36	chr19:36805600-36815800	Weak transcription	NHEK	skin
37	chr19:36805800-36815200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:36805800-36815800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:36805800-36815800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr19:36805800-36816400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr19:36805800-36821000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr19:36806000-36809200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr19:36806400-36809200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:36806400-36811600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:36806400-36820600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr19:36806600-36811400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:36806600-36811600	Strong transcription	Fetal Stomach	stomach
48	chr19:36806600-36821000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:36806600-36822000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:36806800-36810400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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