Variant report

Variant	rs12594139
Chromosome Location	chr15:44586453-44586454
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44586214..44590579-chr15:44718275..44720991,4	K562	blood:

Variant related genes	Relation type
ENSG00000259595	Chromatin interaction
ENSG00000137770	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10152710	0.88[EUR][1000 genomes]
rs1021800	0.88[EUR][1000 genomes]
rs10467977	0.94[EUR][1000 genomes]
rs12591178	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12591581	0.88[EUR][1000 genomes]
rs12591811	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12592995	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	0.88[EUR][1000 genomes]
rs12594167	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]
rs12594645	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12594746	0.94[EUR][1000 genomes]
rs12595484	0.91[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]
rs2303577	0.88[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	0.94[EUR][1000 genomes]
rs3784567	0.94[EUR][1000 genomes]
rs3809471	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816928	0.94[EUR][1000 genomes]
rs3986142	0.94[EUR][1000 genomes]
rs3986143	0.94[EUR][1000 genomes]
rs4415978	0.94[EUR][1000 genomes]
rs4477677	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4577056	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924746	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];0.96[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[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7162671	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7162802	0.91[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[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166278	0.94[EUR][1000 genomes]
rs7166945	0.94[EUR][1000 genomes]
rs7167752	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169333	0.94[EUR][1000 genomes]
rs7170248	0.94[EUR][1000 genomes]
rs7172106	0.94[EUR][1000 genomes]
rs7175200	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178318	0.94[EUR][1000 genomes]
rs7179894	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7181772	0.94[EUR][1000 genomes]
rs7183109	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8023453	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[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	0.94[EUR][1000 genomes]
rs8027036	0.94[EUR][1000 genomes]
rs8028509	0.94[EUR][1000 genomes]
rs8028907	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8032079	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8037395	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs883943	0.94[EUR][1000 genomes]
rs9672237	0.94[EUR][1000 genomes]
rs9673085	0.94[EUR][1000 genomes]
rs9806725	0.89[EUR][1000 genomes];0.98[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:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44582000-44588800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:44582000-44589000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:44582000-44591200	Weak transcription	Spleen	Spleen
4	chr15:44582000-44592000	Weak transcription	Esophagus	oesophagus
5	chr15:44582000-44602000	Weak transcription	Gastric	stomach
6	chr15:44582000-44639400	Weak transcription	Lung	lung
7	chr15:44582600-44587800	Weak transcription	Stomach Mucosa	stomach
8	chr15:44582800-44588400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:44582800-44588800	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:44582800-44588800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:44582800-44589200	Weak transcription	Colonic Mucosa	Colon
12	chr15:44582800-44672200	Weak transcription	HSMM	muscle
13	chr15:44583000-44587200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr15:44583000-44587800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:44583000-44587800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:44583000-44587800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:44583000-44587800	Weak transcription	A549	lung
18	chr15:44583000-44588000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:44583000-44588000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:44583000-44588000	Weak transcription	HMEC	breast
21	chr15:44583000-44588200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:44583000-44588200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:44583000-44588200	Weak transcription	Adipose Nuclei	Adipose
24	chr15:44583000-44588200	Weak transcription	Fetal Intestine Large	intestine
25	chr15:44583000-44588400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:44583000-44588400	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:44583000-44588400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr15:44583000-44588400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:44583000-44588400	Weak transcription	Fetal Kidney	kidney
30	chr15:44583000-44588800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:44583000-44588800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:44583000-44588800	Weak transcription	NHDF-Ad	bronchial
33	chr15:44583000-44589200	Weak transcription	HUVEC	blood vessel
34	chr15:44583000-44639400	Weak transcription	Fetal Lung	lung
35	chr15:44583200-44587400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:44583200-44587800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:44583200-44588200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:44583200-44588200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr15:44583200-44592400	Weak transcription	Aorta	Aorta
40	chr15:44583200-44592800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:44583200-44600800	Weak transcription	Fetal Thymus	thymus
42	chr15:44583200-44639200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr15:44583600-44587400	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:44583600-44587600	Weak transcription	Small Intestine	intestine
45	chr15:44583600-44587800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:44583600-44588000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:44583600-44588200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:44583600-44588200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:44583600-44588200	Weak transcription	Left Ventricle	heart
50	chr15:44583600-44588200	Weak transcription	Psoas Muscle	Psoas

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