Variant report

Variant	rs17470952
Chromosome Location	chr15:77700916-77700917
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	chr15:77700084..77701630-chr15:77707595..77709456,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10519165	1.00[YRI][hapmap]
rs11853696	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854466	0.81[ASN][1000 genomes]
rs11856084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11857330	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11858844	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324016	0.86[ASN][1000 genomes]
rs12324211	0.93[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12324366	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12324795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12898506	1.00[YRI][hapmap]
rs12909771	1.00[YRI][hapmap]
rs12910671	1.00[YRI][hapmap]
rs12912084	0.88[ASN][1000 genomes]
rs12914885	1.00[YRI][hapmap]
rs12917103	1.00[YRI][hapmap]
rs12917359	1.00[YRI][hapmap]
rs13380202	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1493699	0.86[ASN][1000 genomes]
rs16968730	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs16968799	0.86[ASN][1000 genomes]
rs16968897	0.90[CEU][hapmap]
rs17384809	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17385059	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17385296	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17385352	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17469938	1.00[YRI][hapmap]
rs17470529	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17471252	0.85[ASN][1000 genomes]
rs17471280	1.00[YRI][hapmap]
rs17471431	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471480	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17471697	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17471753	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17472200	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2012740	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2012756	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2036896	1.00[YRI][hapmap]
rs2137977	0.81[ASN][1000 genomes]
rs2172587	0.86[ASN][1000 genomes]
rs2292594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2307141	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437977	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2864840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34572155	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap]
rs35651077	0.86[ASN][1000 genomes]
rs3784787	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3784788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4288963	1.00[YRI][hapmap]
rs4592615	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4886857	0.81[ASN][1000 genomes]
rs4886863	0.88[ASN][1000 genomes]
rs4886864	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886865	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56097641	0.84[EUR][1000 genomes]
rs59362734	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59386622	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60079927	0.81[ASN][1000 genomes]
rs62007297	0.90[ASN][1000 genomes]
rs62010566	0.86[ASN][1000 genomes]
rs7182221	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs74025105	0.81[ASN][1000 genomes]
rs74026910	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74026912	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74026913	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74026918	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74026923	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs74026925	0.90[EUR][1000 genomes]
rs74026926	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8035526	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs907398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv482689	chr15:77576396-77731559	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv1792043	chr15:77664901-77708316	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17470952	HMG20A	cis	parietal	SCAN
rs17470952	TSPAN3	Cis_1M	lymphoblastoid	RTeQTL
rs17470952	CYP1A2	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77675000-77709400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:77691600-77703000	Weak transcription	Fetal Heart	heart
3	chr15:77695600-77701600	Weak transcription	GM12878-XiMat	blood
4	chr15:77695600-77701800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:77695600-77701800	Weak transcription	Brain Angular Gyrus	brain
6	chr15:77695600-77702200	Weak transcription	K562	blood
7	chr15:77695600-77702400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:77695600-77705000	Weak transcription	HSMMtube	muscle
9	chr15:77695600-77707800	Weak transcription	NHLF	lung
10	chr15:77695600-77709200	Weak transcription	HMEC	breast
11	chr15:77695800-77701600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:77695800-77709400	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:77696200-77708200	Weak transcription	HSMM	muscle
14	chr15:77696400-77701600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:77696400-77701800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:77696800-77701800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:77696800-77701800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:77696800-77702000	Weak transcription	Osteobl	bone
19	chr15:77696800-77708000	Weak transcription	NHDF-Ad	bronchial
20	chr15:77697000-77701600	Weak transcription	Primary T cells from cord blood	blood
21	chr15:77697400-77701800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:77698400-77701600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:77698600-77701600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:77698600-77701800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:77698600-77711200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:77698800-77701600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:77698800-77702400	Weak transcription	Psoas Muscle	Psoas
28	chr15:77699000-77708000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr15:77699200-77701400	Weak transcription	Primary B cells from cord blood	blood
30	chr15:77699200-77701800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:77699400-77702400	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:77699800-77701200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr15:77699800-77702600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:77700000-77703000	Weak transcription	Fetal Intestine Small	intestine

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