Variant report

Variant	rs7210990
Chromosome Location	chr17:16170764-16170765
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1029809	0.88[CEU][hapmap];0.82[YRI][hapmap];0.94[EUR][1000 genomes]
rs10852834	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078337	0.90[EUR][1000 genomes]
rs11650283	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs11650427	0.88[CEU][hapmap];0.82[YRI][hapmap];0.95[EUR][1000 genomes]
rs11650956	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11651578	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11651955	0.86[ASN][1000 genomes]
rs11653585	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs11653650	0.94[EUR][1000 genomes]
rs11654658	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11655325	0.82[EUR][1000 genomes]
rs11656811	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11868284	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12150564	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12936233	0.84[CEU][hapmap];0.82[YRI][hapmap];0.92[EUR][1000 genomes]
rs12936529	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12938394	0.81[EUR][1000 genomes]
rs12938397	0.91[EUR][1000 genomes]
rs12938878	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12939078	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12945855	0.84[CEU][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes]
rs12945877	0.85[ASN][1000 genomes]
rs12946619	0.84[CEU][hapmap]
rs12946717	0.85[ASN][1000 genomes]
rs12948244	0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs12948905	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1476810	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs15739	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs178787	0.80[CEU][hapmap]
rs178791	0.82[YRI][hapmap]
rs1963811	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2014604	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs2109262	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2324306	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2324307	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3112511	0.81[CEU][hapmap]
rs3112513	0.81[CEU][hapmap]
rs35565381	0.80[EUR][1000 genomes]
rs35762856	0.85[ASN][1000 genomes]
rs3785620	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3785621	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap]
rs3785622	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3785623	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs3785625	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3785626	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4470185	0.80[CEU][hapmap]
rs4791665	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs4792728	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4792729	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4792730	0.82[EUR][1000 genomes]
rs4792731	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4792732	0.83[ASN][1000 genomes]
rs56269147	0.80[EUR][1000 genomes]
rs56326304	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57381510	0.84[ASN][1000 genomes]
rs62072528	0.94[EUR][1000 genomes]
rs6502498	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6502499	0.82[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7215071	0.93[EUR][1000 genomes]
rs7219687	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs7225920	0.82[EUR][1000 genomes]
rs8074727	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9747114	0.81[EUR][1000 genomes]
rs9890539	0.91[CHB][hapmap]
rs9909022	0.94[EUR][1000 genomes]
rs9910148	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9914734	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9916220	0.94[EUR][1000 genomes]
rs9944524	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	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
7	nsv528263	chr17:16097430-16196996	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
8	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
9	nsv907719	chr17:16161036-16185122	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7210990	ZSWIM7	cis	Muscle Skeletal	GTEx
rs7210990	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs7210990	ADORA2B	cis	Artery Tibial	GTEx
rs7210990	ADORA2B	cis	Esophagus Muscularis	GTEx
rs7210990	LOC125150	cis	lesional skin	skin_eQTL
rs7210990	CENPV	cis	Artery Tibial	GTEx
rs7210990	PRR6	cis	multi-tissue	Pritchard
rs7210990	ADORA2B	cis	Muscle Skeletal	GTEx
rs7210990	LOC125150	cis	uninvolved skin	skin_eQTL
rs7210990	ADORA2B	cis	Nerve Tibial	GTEx
rs7210990	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs7210990	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs7210990	LOC125150	cis	normal skin	skin_eQTL
rs7210990	ADORA2B	cis	Thyroid	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16133800-16176200	Weak transcription	NHEK	skin
2	chr17:16154400-16176600	Weak transcription	Hela-S3	cervix
3	chr17:16157400-16185200	Weak transcription	Gastric	stomach
4	chr17:16159200-16178400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr17:16159400-16189200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr17:16159600-16172800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr17:16159600-16188800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr17:16159600-16189000	Weak transcription	Brain Anterior Caudate	brain
9	chr17:16159800-16172800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr17:16160000-16183000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr17:16160400-16188400	Weak transcription	Liver	Liver
12	chr17:16163200-16171200	Weak transcription	Fetal Lung	lung
13	chr17:16163400-16189200	Weak transcription	Left Ventricle	heart
14	chr17:16163600-16189200	Weak transcription	Pancreas	Pancrea
15	chr17:16163800-16171400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr17:16164000-16170800	Weak transcription	Fetal Thymus	thymus
17	chr17:16164000-16171400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:16164000-16176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr17:16164000-16176400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:16164000-16180800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr17:16164000-16182400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr17:16164000-16182400	Weak transcription	Fetal Muscle Leg	muscle
23	chr17:16164000-16185000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:16164000-16189000	Weak transcription	Fetal Brain Female	brain
25	chr17:16164000-16189000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr17:16164200-16171200	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr17:16164200-16182200	Weak transcription	Fetal Stomach	stomach
28	chr17:16164600-16176000	Weak transcription	Fetal Intestine Small	intestine
29	chr17:16164600-16182200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:16165400-16171200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:16166200-16205400	Weak transcription	Brain Hippocampus Middle	brain
32	chr17:16168200-16171600	Enhancers	Duodenum Mucosa	Duodenum
33	chr17:16168600-16188800	Weak transcription	Fetal Intestine Large	intestine
34	chr17:16169200-16176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr17:16170000-16173000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:16170200-16171000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr17:16170200-16171200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr17:16170200-16171200	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr17:16170200-16171200	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr17:16170200-16171400	Enhancers	Primary B cells from cord blood	blood
41	chr17:16170200-16172000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr17:16170200-16172600	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr17:16170200-16173200	Enhancers	Primary B cells from peripheral blood	blood
44	chr17:16170400-16171200	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr17:16170600-16170800	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr17:16170600-16171000	Enhancers	HepG2	liver
47	chr17:16170600-16171200	Enhancers	Primary T cells fromperipheralblood	blood
48	chr17:16170600-16171200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr17:16170600-16171200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr17:16170600-16171200	Enhancers	GM12878-XiMat	blood

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