Variant report

Variant	rs17167312
Chromosome Location	chr7:7443602-7443603
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10085771	0.86[EUR][1000 genomes]
rs10085830	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10225403	1.00[CEU][hapmap]
rs10226811	0.83[EUR][1000 genomes]
rs10229355	0.80[EUR][1000 genomes]
rs10234561	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10234818	0.83[EUR][1000 genomes]
rs10236946	1.00[CEU][hapmap];0.96[TSI][hapmap]
rs10244711	0.89[CEU][hapmap]
rs10246954	1.00[CEU][hapmap]
rs10247676	0.91[CEU][hapmap];0.96[TSI][hapmap];0.80[EUR][1000 genomes]
rs10248825	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10250746	0.91[CEU][hapmap]
rs10250756	0.91[CEU][hapmap]
rs10255190	0.94[EUR][1000 genomes]
rs10255201	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10257694	1.00[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs10263223	1.00[CEU][hapmap]
rs10268438	0.86[EUR][1000 genomes]
rs10269244	0.87[EUR][1000 genomes]
rs10280546	1.00[CEU][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs10486160	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10486161	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10486163	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10486165	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10486166	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs10486168	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10486171	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs10486173	0.91[CEU][hapmap]
rs10486175	0.81[CEU][hapmap]
rs10486176	0.81[CEU][hapmap]
rs11977826	0.83[CEU][hapmap]
rs12668945	0.91[CEU][hapmap]
rs12702613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1294597	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1294598	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1294599	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1294601	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1294602	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1294603	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1296103	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13227277	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13230547	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13307616	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16878046	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16878052	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap]
rs16878062	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16878455	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs17151541	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17151547	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17167323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17167601	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17167624	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17167625	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17167690	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17167804	1.00[CEU][hapmap]
rs17168096	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs17168127	0.84[EUR][1000 genomes]
rs17168144	0.81[EUR][1000 genomes]
rs17168145	0.81[EUR][1000 genomes]
rs17168152	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs17168215	0.81[EUR][1000 genomes]
rs17168217	0.91[CEU][hapmap]
rs17168290	0.81[CEU][hapmap]
rs17168295	0.81[CEU][hapmap];0.81[GIH][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap]
rs17168350	0.81[CEU][hapmap];0.81[GIH][hapmap];0.85[MKK][hapmap];0.84[TSI][hapmap]
rs17168367	0.81[CEU][hapmap]
rs17168368	0.81[CEU][hapmap]
rs17168369	0.81[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap]
rs17510752	0.81[CEU][hapmap]
rs1860725	0.86[EUR][1000 genomes]
rs1997518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108065	0.81[CEU][hapmap]
rs2109772	1.00[CEU][hapmap]
rs2286839	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28493883	0.83[EUR][1000 genomes]
rs28505765	0.87[EUR][1000 genomes]
rs28669774	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34889595	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35462098	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3757528	0.92[TSI][hapmap]
rs3779375	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs4320465	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap]
rs4543457	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55798422	0.85[EUR][1000 genomes]
rs55827101	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55980077	0.85[EUR][1000 genomes]
rs56022797	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56084871	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56330916	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57521604	0.81[EUR][1000 genomes]
rs57930817	0.83[EUR][1000 genomes]
rs60020853	0.86[EUR][1000 genomes]
rs60120688	0.86[EUR][1000 genomes]
rs60314248	0.81[EUR][1000 genomes]
rs60668247	0.84[EUR][1000 genomes]
rs60977515	0.84[EUR][1000 genomes]
rs61543470	0.81[EUR][1000 genomes]
rs6463692	1.00[CEU][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs6945969	0.91[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs6946064	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6946913	1.00[TSI][hapmap]
rs6947175	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6948300	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6949534	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6953394	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6955328	0.91[CEU][hapmap]
rs6957099	1.00[CEU][hapmap]
rs6957880	0.91[CEU][hapmap];0.92[TSI][hapmap]
rs6960158	0.82[EUR][1000 genomes]
rs6962455	1.00[ASW][hapmap];0.91[CEU][hapmap];0.81[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6963106	0.91[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6964749	0.81[EUR][1000 genomes]
rs6965546	0.91[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs6967835	1.00[CEU][hapmap]
rs6968394	0.90[CEU][hapmap]
rs6971367	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6971414	0.86[EUR][1000 genomes]
rs6971456	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs6972142	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6975571	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6977661	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6979055	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs725933	0.84[EUR][1000 genomes]
rs725934	1.00[CEU][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs73334107	0.84[EUR][1000 genomes]
rs73346330	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7459128	0.81[CEU][hapmap];0.88[TSI][hapmap]
rs7778212	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7780426	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7780713	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7789255	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7798119	0.81[CEU][hapmap]
rs7804915	0.87[EUR][1000 genomes]
rs7807121	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs7812265	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs929378	0.81[CEU][hapmap]
rs972766	0.81[CEU][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023133	chr7:6854098-7516700	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv869091	chr7:6927461-7567820	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv949293	chr7:6990891-7711883	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv1032813	chr7:7053923-7497484	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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 miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1030246	chr7:7053923-7569633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv1019498	chr7:7053923-7668373	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
7	nsv538721	chr7:7053923-7668373	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers 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 miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
9	esv2758102	chr7:7209911-7493901	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	esv2759505	chr7:7209911-7493901	Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv469770	chr7:7261414-7453821	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv887470	chr7:7310023-7655094	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv606039	chr7:7317590-7497676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1020988	chr7:7348251-7497484	ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv887472	chr7:7405069-7680697	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
16	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17167312	COL28A1	cis	cerebellum	SCAN
rs17167312	MIOS	cis	parietal	SCAN
rs17167312	COL28A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7433800-7444000	Weak transcription	Pancreas	Pancrea
2	chr7:7443600-7444000	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr7:7443600-7444200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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