Variant report

Variant	rs7223476
Chromosome Location	chr17:20215352-20215353
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10491107	0.87[ASW][hapmap];0.82[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204300	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11653630	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11653869	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11654942	0.86[ASN][1000 genomes]
rs11657161	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11658116	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11868116	0.82[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11869258	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603372	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938355	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12942627	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12949481	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12950564	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1373146	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16960697	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs1859407	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1992561	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013443	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs2042046	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs2107565	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs2158472	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2189709	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs2526465	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526466	1.00[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2526476	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526477	0.81[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526478	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2526481	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs2703771	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs2703776	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703777	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703781	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703786	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2703788	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2703800	0.87[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs2703803	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2703805	0.82[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs2703807	0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs2703814	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs3850779	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3850780	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925087	0.82[CEU][hapmap];0.94[CHB][hapmap]
rs4925090	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs57837691	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67217337	0.91[ASN][1000 genomes]
rs7212571	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7216599	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs7219615	0.80[ASN][1000 genomes]
rs73309111	0.95[ASN][1000 genomes]
rs733794	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757494	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs757495	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8066143	0.81[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs8071274	0.87[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8078716	0.82[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs8080649	0.82[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs9893832	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs9901336	0.83[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap]
rs9912844	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1067100	chr17:20007480-20464520	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv543260	chr17:20007480-20464520	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv428669	chr17:20071969-20245033	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1064854	chr17:20086562-20225751	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2761953	chr17:20086562-20225763	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv574581	chr17:20088492-20699545	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv1065758	chr17:20141912-20464366	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv543262	chr17:20141912-20464366	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
10	nsv1057389	chr17:20158343-20256498	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv427993	chr17:20171398-20482061	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	nsv916440	chr17:20171468-20839266	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
13	nsv520772	chr17:20184501-20522444	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
14	nsv521025	chr17:20198024-20514921	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7223476	C2orf81	trans	cerebellum	SCAN
rs7223476	CYTSB	cis	cerebellum	SCAN
rs7223476	TMEM11	cis	cerebellum	SCAN
rs7223476	PAPSS2	trans	lymphoblastoid	seeQTL
rs7223476	KRT16P3	cis	Esophagus Mucosa	GTEx
rs7223476	CYTSB	cis	parietal	SCAN
rs7223476	AKAP10	cis	multi-tissue	Pritchard
rs7223476	AKAP10	cis	Lymphoblastoid	GTEx
rs7223476	AKAP10	cis	lymphoblastoid	seeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20187800-20223800	Weak transcription	Pancreas	Pancrea
2	chr17:20201000-20220000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:20204400-20216800	Weak transcription	Gastric	stomach
4	chr17:20210800-20223800	Weak transcription	Colonic Mucosa	Colon
5	chr17:20210800-20223800	Weak transcription	Esophagus	oesophagus
6	chr17:20211000-20215800	Weak transcription	Brain Angular Gyrus	brain
7	chr17:20211000-20215800	Weak transcription	Brain Substantia Nigra	brain
8	chr17:20211000-20216000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr17:20211000-20216600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr17:20211000-20216600	Weak transcription	Aorta	Aorta
11	chr17:20211000-20216800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr17:20211000-20216800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr17:20211000-20217000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:20211000-20217000	Weak transcription	NHEK	skin
15	chr17:20211000-20217200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:20211000-20217200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr17:20211000-20218600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr17:20211000-20218600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr17:20211000-20219600	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr17:20211000-20223000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:20211000-20223800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:20211000-20223800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:20211000-20224000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr17:20211000-20224000	Weak transcription	HMEC	breast
25	chr17:20211200-20215800	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr17:20211200-20216000	Weak transcription	GM12878-XiMat	blood
27	chr17:20211200-20216000	Weak transcription	NH-A	brain
28	chr17:20211200-20217000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr17:20211200-20217200	Weak transcription	Fetal Brain Female	brain
30	chr17:20211200-20221600	Weak transcription	Small Intestine	intestine
31	chr17:20211200-20223800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr17:20211200-20224000	Weak transcription	Fetal Intestine Large	intestine
33	chr17:20211400-20220800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr17:20211400-20224000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr17:20211600-20217400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr17:20211600-20218000	Weak transcription	Fetal Intestine Small	intestine
37	chr17:20211600-20221800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:20211600-20224000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr17:20212200-20216600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr17:20212200-20222000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:20212400-20219800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr17:20212600-20216600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:20212600-20217000	Weak transcription	Osteobl	bone
44	chr17:20212800-20215800	Weak transcription	Brain Anterior Caudate	brain
45	chr17:20212800-20218400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr17:20213000-20216000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:20213000-20217200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:20213000-20217200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:20213000-20217400	Weak transcription	Brain Germinal Matrix	brain
50	chr17:20213000-20218800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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