Variant report

Variant	rs15739
Chromosome Location	chr17:16229232-16229233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16228167..16229725-chr17:16230867..16233220,2	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10852834	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11078337	0.82[EUR][1000 genomes]
rs11650283	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650427	0.83[TSI][hapmap]
rs11650956	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651578	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11651955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653585	0.91[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs11654658	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11655906	0.84[EUR][1000 genomes]
rs11655907	0.84[EUR][1000 genomes]
rs11656811	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11868284	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12150564	0.83[ASN][1000 genomes]
rs12449629	0.82[EUR][1000 genomes]
rs12936233	0.83[TSI][hapmap]
rs12936529	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938397	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12938878	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12939078	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12945855	0.83[TSI][hapmap]
rs12945877	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12946717	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12947973	0.81[EUR][1000 genomes]
rs12948680	0.82[EUR][1000 genomes]
rs12948905	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476810	0.90[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16959630	1.00[CHD][hapmap];0.88[JPT][hapmap]
rs1963811	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2014604	0.82[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap]
rs2109262	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2324306	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2324307	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28862997	0.80[EUR][1000 genomes]
rs3112511	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs3112513	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs35762856	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3785620	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3785621	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap]
rs3785622	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785623	0.82[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap]
rs3785625	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785626	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4791665	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap]
rs4792728	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792729	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4792731	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4792732	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4792735	0.85[EUR][1000 genomes]
rs56326304	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62074191	0.86[ASN][1000 genomes]
rs62074192	0.86[ASN][1000 genomes]
rs6502498	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6502499	0.82[CEU][hapmap];0.83[CHB][hapmap]
rs7210990	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7219687	0.82[CEU][hapmap];0.83[CHB][hapmap];0.83[GIH][hapmap]
rs7224367	0.83[EUR][1000 genomes]
rs7477	0.89[TSI][hapmap]
rs8074246	0.86[ASN][1000 genomes]
rs8074727	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9747806	0.89[ASN][1000 genomes]
rs9890539	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs9890867	0.90[EUR][1000 genomes]
rs9893005	0.84[EUR][1000 genomes]
rs9910148	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9914734	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9944524	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[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	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv1063764	chr17:16171649-16662914	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs15739	ELAC2	cis	parietal	SCAN
rs15739	PRR6	cis	multi-tissue	Pritchard
rs15739	TRPV2	cis	cerebellum	SCAN
rs15739	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs15739	CENPV	cis	Artery Tibial	GTEx
rs15739	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs15739	ZSWIM7	cis	Muscle Skeletal	GTEx
rs15739	TRPV2	cis	parietal	SCAN
rs15739	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs15739	ADORA2B	cis	Muscle Skeletal	GTEx
rs15739	PRPSAP2	cis	parietal	SCAN
rs15739	ADORA2B	cis	Artery Tibial	GTEx
rs15739	TRPV2	cis	Frontal Cortex	GTEx
rs15739	CENPV	cis	parietal	SCAN
rs15739	LOC125150	cis	uninvolved skin	skin_eQTL
rs15739	CENPV	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16190600-16229600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr17:16197800-16230000	Weak transcription	Brain Angular Gyrus	brain
3	chr17:16201000-16232400	Weak transcription	Hela-S3	cervix
4	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
5	chr17:16205800-16245600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr17:16206000-16232200	Weak transcription	HMEC	breast
7	chr17:16206000-16245800	Weak transcription	Brain Anterior Caudate	brain
8	chr17:16206000-16246000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr17:16207400-16232400	Weak transcription	Right Atrium	heart
10	chr17:16209000-16245600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr17:16214600-16233000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr17:16214600-16255200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr17:16216400-16231000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr17:16216800-16229600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr17:16216800-16232400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr17:16217000-16232400	Weak transcription	Gastric	stomach
17	chr17:16217000-16246000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr17:16217200-16255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr17:16217400-16232400	Weak transcription	A549	lung
20	chr17:16217600-16229400	Weak transcription	Primary hematopoietic stem cells	blood
21	chr17:16217600-16232600	Weak transcription	Small Intestine	intestine
22	chr17:16217800-16230200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr17:16218000-16231800	Strong transcription	Fetal Intestine Small	intestine
24	chr17:16218000-16232000	Strong transcription	Fetal Stomach	stomach
25	chr17:16218000-16232400	Weak transcription	NHLF	lung
26	chr17:16219200-16246000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr17:16220400-16229400	Weak transcription	Osteobl	bone
28	chr17:16220800-16229400	Weak transcription	HepG2	liver
29	chr17:16220800-16232400	Weak transcription	Stomach Mucosa	stomach
30	chr17:16221000-16230000	Weak transcription	Aorta	Aorta
31	chr17:16221200-16232800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:16221400-16232400	Weak transcription	NHEK	skin
33	chr17:16222800-16245600	Weak transcription	Right Ventricle	heart
34	chr17:16224600-16232400	Weak transcription	HUVEC	blood vessel
35	chr17:16225600-16230400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr17:16225800-16245800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr17:16226000-16230600	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr17:16226000-16230600	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr17:16226000-16230800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr17:16226000-16231000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr17:16226600-16232400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr17:16226600-16232400	Weak transcription	NHDF-Ad	bronchial
43	chr17:16226600-16245600	Weak transcription	Fetal Kidney	kidney
44	chr17:16227200-16229800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr17:16227200-16230000	Weak transcription	HSMM	muscle
46	chr17:16227200-16230600	Strong transcription	Primary T cells from cord blood	blood
47	chr17:16227400-16230600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr17:16227400-16232600	Weak transcription	Fetal Heart	heart
49	chr17:16227600-16230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr17:16227600-16230600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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