Variant report

Variant	rs3112513
Chromosome Location	chr17:16208812-16208813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs11650283	0.82[CEU][hapmap];0.83[GIH][hapmap]
rs11650956	0.84[EUR][1000 genomes]
rs11651578	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs11652044	0.82[EUR][1000 genomes]
rs11653500	0.86[EUR][1000 genomes]
rs11654658	0.89[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs11655325	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11655906	0.83[EUR][1000 genomes]
rs11655907	0.83[EUR][1000 genomes]
rs11656811	0.89[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]
rs11868284	0.81[CEU][hapmap];0.91[GIH][hapmap];0.83[EUR][1000 genomes]
rs12150285	0.81[EUR][1000 genomes]
rs12449629	0.86[EUR][1000 genomes]
rs12938394	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12938878	0.83[EUR][1000 genomes]
rs12939078	0.84[EUR][1000 genomes]
rs12945959	0.86[EUR][1000 genomes]
rs12946619	0.88[ASW][hapmap];0.85[GIH][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs12947973	0.85[EUR][1000 genomes]
rs12948244	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12948680	0.85[EUR][1000 genomes]
rs12949255	0.83[EUR][1000 genomes]
rs12949537	0.82[EUR][1000 genomes]
rs1476810	0.84[GIH][hapmap]
rs15739	0.82[CEU][hapmap];0.84[GIH][hapmap]
rs178785	0.82[EUR][1000 genomes]
rs178787	0.83[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1963811	0.81[EUR][1000 genomes]
rs2014604	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2074995	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2109262	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs2324142	0.88[LWK][hapmap];0.80[MKK][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap]
rs2324307	0.82[EUR][1000 genomes]
rs28516015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28862997	0.84[EUR][1000 genomes]
rs3095171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112511	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][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];0.98[ASN][1000 genomes]
rs3112521	0.90[GIH][hapmap]
rs3112524	0.90[GIH][hapmap]
rs3112526	0.90[GIH][hapmap]
rs3112527	0.90[GIH][hapmap];0.81[MEX][hapmap]
rs34331598	0.86[EUR][1000 genomes]
rs35565381	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3785621	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3785622	0.84[EUR][1000 genomes]
rs3785623	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3785625	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3785626	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs4470185	0.85[GIH][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs4791665	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4792728	0.85[CEU][hapmap];0.91[GIH][hapmap];0.82[EUR][1000 genomes]
rs4792729	0.82[EUR][1000 genomes]
rs4792730	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4792731	0.89[CEU][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs4792735	0.83[EUR][1000 genomes]
rs56269147	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62072527	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6502499	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7210990	0.81[CEU][hapmap]
rs7219687	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7223428	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7224367	0.87[EUR][1000 genomes]
rs7225920	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8073259	0.88[ASW][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8074727	0.83[EUR][1000 genomes]
rs917609	0.90[GIH][hapmap]
rs9303135	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9747114	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9890539	0.92[CEU][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs9893005	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9914734	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs9944524	0.89[CEU][hapmap];0.91[GIH][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3326983	chr17:16138963-16210147	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	21 gene(s)	inside rSNPs	diseases
7	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:19)

SNP	Gene	Cis/trans	Tissue	Source
rs3112513	CENPV	cis	parietal	SCAN
rs3112513	PRR6	cis	multi-tissue	Pritchard
rs3112513	ZSWIM7	cis	Muscle Skeletal	GTEx
rs3112513	LOC125150	cis	lesional skin	skin_eQTL
rs3112513	TRPV2	cis	cerebellum	SCAN
rs3112513	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs3112513	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs3112513	ADORA2B	cis	Nerve Tibial	GTEx
rs3112513	CENPV	cis	Artery Tibial	GTEx
rs3112513	PRPSAP2	cis	parietal	SCAN
rs3112513	LOC125150	cis	uninvolved skin	skin_eQTL
rs3112513	ADORA2B	cis	Thyroid	GTEx
rs3112513	ADORA2B	cis	Artery Tibial	GTEx
rs3112513	TRPV2	cis	parietal	SCAN
rs3112513	ADORA2B	cis	Muscle Skeletal	GTEx
rs3112513	TTC19	cis	lymphoblastoid	seeQTL
rs3112513	ELAC2	cis	parietal	SCAN
rs3112513	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs3112513	ADORA2B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16189400-16216600	Weak transcription	Fetal Brain Female	brain
2	chr17:16190600-16229600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr17:16190800-16216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:16190800-16220800	Weak transcription	Aorta	Aorta
5	chr17:16191400-16218400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr17:16191400-16219400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr17:16191400-16226000	Weak transcription	HSMMtube	muscle
8	chr17:16191600-16216800	Weak transcription	Fetal Kidney	kidney
9	chr17:16191800-16217200	Weak transcription	HSMM	muscle
10	chr17:16192800-16229000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr17:16194000-16216400	Weak transcription	GM12878-XiMat	blood
12	chr17:16197800-16230000	Weak transcription	Brain Angular Gyrus	brain
13	chr17:16198400-16220400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr17:16200800-16216600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:16200800-16216600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr17:16200800-16228200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr17:16201000-16232400	Weak transcription	Hela-S3	cervix
18	chr17:16201200-16213600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:16201200-16214000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:16201200-16214200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr17:16201200-16223200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr17:16201400-16214000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr17:16201400-16216200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:16201600-16228800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr17:16201600-16246400	Weak transcription	Fetal Brain Male	brain
26	chr17:16201800-16221000	Weak transcription	Colonic Mucosa	Colon
27	chr17:16202000-16214000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr17:16202000-16214200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:16202000-16214200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr17:16202000-16214200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr17:16202200-16214000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr17:16202200-16214200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr17:16202200-16216400	Weak transcription	K562	blood
34	chr17:16202200-16216600	Weak transcription	Pancreas	Pancrea
35	chr17:16203000-16210800	Strong transcription	Fetal Muscle Leg	muscle
36	chr17:16203000-16211000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr17:16203200-16210800	Strong transcription	Primary T cells from cord blood	blood
38	chr17:16203200-16213200	Strong transcription	Fetal Stomach	stomach
39	chr17:16203600-16210200	Weak transcription	Stomach Mucosa	stomach
40	chr17:16203600-16214000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr17:16203600-16214200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:16203600-16228800	Weak transcription	Primary B cells from cord blood	blood
43	chr17:16203800-16216400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr17:16203800-16216600	Weak transcription	Small Intestine	intestine
45	chr17:16204000-16219400	Weak transcription	Brain Germinal Matrix	brain
46	chr17:16204200-16220000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:16204200-16228800	Weak transcription	Brain Substantia Nigra	brain
48	chr17:16204400-16215400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr17:16204600-16226000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr17:16205400-16228800	Weak transcription	Colon Smooth Muscle	Colon

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