Variant report

Variant	rs17493655
Chromosome Location	chr2:98898220-98898221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10176056	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10181000	0.87[CHB][hapmap]
rs10190336	0.84[ASN][1000 genomes]
rs10199476	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs10201994	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202618	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10203437	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11124096	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs11124107	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11124121	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11673807	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11679920	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11889349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs11891512	0.82[ASN][1000 genomes]
rs11895654	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs11901562	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12478763	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12478769	0.82[ASN][1000 genomes]
rs12622324	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12624294	1.00[ASN][1000 genomes]
rs12712256	0.92[ASN][1000 genomes]
rs12993718	0.82[ASN][1000 genomes]
rs12999985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13013876	0.82[ASN][1000 genomes]
rs13014142	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13033263	0.82[ASN][1000 genomes]
rs13394706	0.87[CHB][hapmap]
rs13408372	0.85[CHB][hapmap]
rs13415414	1.00[ASN][1000 genomes]
rs13428221	0.83[ASN][1000 genomes]
rs1451251	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1466944	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.93[ASN][1000 genomes]
rs1504679	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17427684	0.98[ASN][1000 genomes]
rs17428056	1.00[ASN][1000 genomes]
rs17429208	0.87[CHB][hapmap];0.87[MEX][hapmap]
rs17493788	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1875880	0.98[ASN][1000 genomes]
rs2102270	0.87[CHB][hapmap]
rs2122756	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs2202387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2221416	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292118	0.87[CHB][hapmap]
rs2292119	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3731659	0.98[ASN][1000 genomes]
rs4374424	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4389366	0.92[ASN][1000 genomes]
rs4455212	1.00[CHB][hapmap]
rs4477970	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4479470	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4494805	0.82[ASN][1000 genomes]
rs4535095	0.81[ASN][1000 genomes]
rs4608580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4632400	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs4851122	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851123	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851124	0.98[ASN][1000 genomes]
rs4851935	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4851951	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4851952	0.82[ASN][1000 genomes]
rs4851954	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4851955	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851959	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851960	0.91[ASN][1000 genomes]
rs62157914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543419	1.00[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6543459	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66464436	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715989	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6725543	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6742930	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6747344	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6747410	0.87[CHB][hapmap];0.80[CHD][hapmap]
rs6750975	0.98[ASN][1000 genomes]
rs6754222	0.81[CHB][hapmap]
rs72933220	1.00[ASN][1000 genomes]
rs7572757	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574218	0.82[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7589018	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598554	0.92[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7606070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7606220	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs937726	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1002366	chr2:98877050-98904494	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv961333	chr2:98894552-98898661	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17493655	ZNF514	cis	parietal	SCAN
rs17493655	MRPS5	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98894600-98898400	Enhancers	Esophagus	oesophagus
2	chr2:98896800-98898600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:98897200-98898600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:98897200-98898600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:98897200-98898600	Enhancers	Stomach Mucosa	stomach
6	chr2:98897400-98898400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:98897600-98899000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:98897800-98898800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:98897800-98899000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr2:98898000-98899200	Enhancers	Colonic Mucosa	Colon
11	chr2:98898000-98899400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:98898200-98898400	Enhancers	Gastric	stomach
13	chr2:98898200-98898600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr2:98898200-98898800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:98898200-98898800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:98898200-98898800	Enhancers	Rectal Mucosa Donor 29	rectum

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