Variant report

Variant	rs12449649
Chromosome Location	chr17:67260926-67260927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1011549	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10445224	0.96[ASN][1000 genomes]
rs10491177	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10512526	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10512527	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs11077445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs112914	0.95[JPT][hapmap]
rs11649744	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11650658	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11650955	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11651815	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11651872	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11652207	0.89[CEU][hapmap];0.80[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11654323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11656456	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11869324	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11871771	0.83[ASW][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.91[TSI][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12450167	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450402	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12450522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12450743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12452340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12937191	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12937947	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12938039	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12938064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12938097	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12940364	0.85[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12941297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12942763	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12942867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12943504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12944980	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12945481	1.00[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]
rs12945908	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12946566	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12946776	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12949267	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12952942	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1550828	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs15886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1990248	0.84[ASN][1000 genomes]
rs2364996	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2441358	0.87[ASN][1000 genomes]
rs34334829	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34609440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34985085	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4310935	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4310936	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs471193	0.95[JPT][hapmap]
rs475283	0.90[JPT][hapmap]
rs476677	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs481876	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs486840	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs488714	0.81[ASN][1000 genomes]
rs494946	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs523505	0.84[ASN][1000 genomes]
rs531586	0.88[JPT][hapmap]
rs534645	0.95[JPT][hapmap]
rs544940	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs557491	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs55773491	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568536	0.90[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs57949169	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58634970	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6501313	0.95[JPT][hapmap]
rs7213377	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7223895	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7225762	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs817121	0.95[JPT][hapmap]
rs817126	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs817127	0.89[ASN][1000 genomes]
rs9646388	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv575932	chr17:67149973-67327806	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	15 gene(s)	inside rSNPs	diseases
2	nsv457889	chr17:67210992-67332355	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
3	nsv575934	chr17:67210992-67332355	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	n/a
4	nsv1055156	chr17:67239695-67272311	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a
5	nsv833527	chr17:67240575-67400871	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv575935	chr17:67256162-67327806	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:67230800-67271800	Weak transcription	Pancreas	Pancrea
2	chr17:67235000-67289000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr17:67236000-67283000	Weak transcription	Ovary	ovary
4	chr17:67236400-67278000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:67236800-67280800	Weak transcription	Brain Angular Gyrus	brain
6	chr17:67236800-67298800	Weak transcription	Psoas Muscle	Psoas
7	chr17:67238800-67278000	Weak transcription	Thymus	Thymus
8	chr17:67239200-67262400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:67240000-67289200	Weak transcription	Esophagus	oesophagus
10	chr17:67240000-67296000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr17:67242000-67265000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr17:67242200-67265000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr17:67242200-67265000	Weak transcription	NHEK	skin
14	chr17:67242400-67289400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr17:67243000-67264800	Weak transcription	NHDF-Ad	bronchial
16	chr17:67243600-67305600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:67244000-67262400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr17:67244000-67321800	Weak transcription	Right Ventricle	heart
19	chr17:67245600-67261600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr17:67245800-67278000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr17:67248000-67284400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr17:67249000-67264600	Weak transcription	Left Ventricle	heart
23	chr17:67249000-67278400	Weak transcription	Fetal Intestine Small	intestine
24	chr17:67250000-67289200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:67250200-67280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr17:67250800-67264600	Weak transcription	Osteobl	bone
27	chr17:67250800-67265200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:67250800-67277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:67251200-67279000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr17:67251400-67264000	Weak transcription	HUVEC	blood vessel
31	chr17:67251400-67264200	Weak transcription	Fetal Intestine Large	intestine
32	chr17:67251400-67264200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr17:67251400-67272000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:67251400-67273000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr17:67251400-67277600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr17:67251400-67277800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr17:67251400-67278000	Weak transcription	Primary T cells from cord blood	blood
38	chr17:67251600-67265800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr17:67251600-67265800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr17:67251600-67274000	Weak transcription	GM12878-XiMat	blood
41	chr17:67251600-67278200	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr17:67251600-67289200	Weak transcription	Brain Anterior Caudate	brain
43	chr17:67251800-67264600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr17:67251800-67264800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr17:67252200-67264600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr17:67252400-67272400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr17:67253200-67278200	Weak transcription	Placenta	Placenta
48	chr17:67255600-67272000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr17:67257600-67278000	Weak transcription	Adipose Nuclei	Adipose
50	chr17:67258600-67264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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