Variant report

Variant	rs12594645
Chromosome Location	chr15:44592847-44592848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10152710	0.88[EUR][1000 genomes]
rs1021800	0.88[GIH][hapmap];0.88[EUR][1000 genomes]
rs10467977	0.94[EUR][1000 genomes]
rs11070426	0.88[GIH][hapmap]
rs12591178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12591581	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12591811	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592995	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs12593125	0.94[EUR][1000 genomes]
rs12593325	0.88[EUR][1000 genomes]
rs12593686	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593943	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594110	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[EUR][1000 genomes]
rs12594139	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12594621	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594746	0.94[EUR][1000 genomes]
rs12595484	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17551416	0.88[EUR][1000 genomes]
rs2055061	0.94[EUR][1000 genomes]
rs2288341	0.88[EUR][1000 genomes]
rs2288342	0.94[EUR][1000 genomes]
rs2303577	0.88[EUR][1000 genomes]
rs2303578	0.82[EUR][1000 genomes]
rs2412883	0.94[EUR][1000 genomes]
rs2412909	0.94[EUR][1000 genomes]
rs2433350	0.94[EUR][1000 genomes]
rs2555353	0.94[EUR][1000 genomes]
rs2556566	0.94[EUR][1000 genomes]
rs2556567	0.88[EUR][1000 genomes]
rs28508235	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28561508	0.94[EUR][1000 genomes]
rs2899113	0.88[EUR][1000 genomes]
rs35555389	0.94[EUR][1000 genomes]
rs3784565	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3784567	0.94[EUR][1000 genomes]
rs3809471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816928	1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes]
rs3986142	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs3986143	0.87[ASW][hapmap];0.92[JPT][hapmap];0.82[LWK][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes]
rs4415978	0.94[EUR][1000 genomes]
rs4477677	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4577056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924746	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs57270586	0.94[EUR][1000 genomes]
rs58956090	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59230801	0.94[EUR][1000 genomes]
rs59997416	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60003667	0.94[EUR][1000 genomes]
rs60399672	0.94[EUR][1000 genomes]
rs61185650	0.94[EUR][1000 genomes]
rs61234123	0.94[EUR][1000 genomes]
rs61258861	0.94[EUR][1000 genomes]
rs61278540	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61329003	0.94[EUR][1000 genomes]
rs61501839	0.94[EUR][1000 genomes]
rs6493103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162802	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7163529	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166278	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7166945	0.94[EUR][1000 genomes]
rs7167752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169333	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7170248	0.94[EUR][1000 genomes]
rs7172106	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7175200	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178318	0.94[EUR][1000 genomes]
rs7179894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181772	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs7183109	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8023453	0.87[ASW][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes]
rs8024623	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8024805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8025727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8025876	0.94[EUR][1000 genomes]
rs8025955	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8026945	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs8027036	0.94[EUR][1000 genomes]
rs8028509	0.94[EUR][1000 genomes]
rs8028907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs883943	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs9672237	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs9673085	1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs9806725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
3	nsv1052511	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv542371	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv3410956	chr15:44425145-44823647	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv2754388	chr15:44479709-44592847	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1044686	chr15:44489534-44697482	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv1043822	chr15:44491220-44686957	Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1035386	chr15:44498905-44677174	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv904177	chr15:44582886-44821843	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44582000-44602000	Weak transcription	Gastric	stomach
2	chr15:44582000-44639400	Weak transcription	Lung	lung
3	chr15:44582800-44672200	Weak transcription	HSMM	muscle
4	chr15:44583000-44639400	Weak transcription	Fetal Lung	lung
5	chr15:44583200-44600800	Weak transcription	Fetal Thymus	thymus
6	chr15:44583200-44639200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr15:44583600-44596000	Weak transcription	Ovary	ovary
8	chr15:44583600-44598200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:44583600-44602000	Weak transcription	Pancreas	Pancrea
10	chr15:44583800-44596800	Weak transcription	Primary T cells from cord blood	blood
11	chr15:44583800-44639200	Weak transcription	Brain Germinal Matrix	brain
12	chr15:44584000-44593800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr15:44584200-44597800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:44584200-44625600	Weak transcription	Fetal Brain Female	brain
15	chr15:44585400-44595800	Weak transcription	Fetal Stomach	stomach
16	chr15:44585400-44628200	Weak transcription	Thymus	Thymus
17	chr15:44586200-44600800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr15:44587800-44594600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr15:44588000-44600800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:44589000-44601200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:44589000-44619000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:44589000-44631600	Weak transcription	Left Ventricle	heart
23	chr15:44589200-44597200	Weak transcription	Brain Substantia Nigra	brain
24	chr15:44589200-44598000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:44589200-44599200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:44589200-44600000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:44589200-44626400	Weak transcription	Fetal Muscle Leg	muscle
28	chr15:44589400-44595400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:44589400-44600200	Weak transcription	Adipose Nuclei	Adipose
30	chr15:44589400-44607000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:44589400-44607600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:44589600-44593000	Weak transcription	A549	lung
33	chr15:44589600-44599600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr15:44589600-44600200	Weak transcription	Fetal Kidney	kidney
35	chr15:44589600-44602200	Weak transcription	Psoas Muscle	Psoas
36	chr15:44589600-44605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:44589600-44617400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:44589800-44593200	Enhancers	K562	blood
39	chr15:44589800-44593400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:44589800-44599800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr15:44589800-44600600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:44589800-44600600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:44589800-44601800	Weak transcription	Osteobl	bone
44	chr15:44589800-44602000	Weak transcription	Right Atrium	heart
45	chr15:44589800-44625200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:44589800-44632000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:44589800-44632400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:44589800-44632400	Weak transcription	NHLF	lung
49	chr15:44591400-44632800	Weak transcription	Hela-S3	cervix
50	chr15:44591800-44593200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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