Variant report

Variant	rs1516708
Chromosome Location	chr4:92502367-92502368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1003265	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10470887	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10516897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs1114290	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1114625	0.80[ASN][1000 genomes]
rs11731403	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11733544	0.81[AMR][1000 genomes]
rs11931400	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11932823	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11932865	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11937905	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11940909	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11941720	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11941818	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11946091	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11946281	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11947273	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12152593	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs12501164	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13110767	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112431	0.87[ASN][1000 genomes]
rs13117758	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13134406	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13135264	0.82[ASN][1000 genomes]
rs13149286	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400351	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs1400352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[ASN][1000 genomes]
rs1533462	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1588986	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs1607078	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17285646	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17841804	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1914239	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1914240	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2048867	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs2138581	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs34451329	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34920942	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34940074	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34982476	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35531607	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4376107	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4426739	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57015636	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57107634	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57546696	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60147430	0.81[EUR][1000 genomes]
rs61143842	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62311874	0.81[ASN][1000 genomes]
rs62311884	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62311910	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6532317	1.00[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[YRI][hapmap]
rs6532321	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs6532322	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6532334	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6532335	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6821624	0.82[ASN][1000 genomes]
rs6822174	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6823252	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6829570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6838394	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841299	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6841361	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6845243	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6852718	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6854814	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7657012	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7666325	0.95[ASN][1000 genomes]
rs7666679	0.88[ASN][1000 genomes]
rs7667244	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs7670961	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7688294	0.85[ASN][1000 genomes]
rs7693738	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs9918048	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869023	chr4:91940838-92935383	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv879572	chr4:92281419-92510827	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv879573	chr4:92281419-92520419	Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv879575	chr4:92322333-92520419	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv879576	chr4:92356118-92651110	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv879579	chr4:92373327-92520419	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv879580	chr4:92373327-92551065	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv879583	chr4:92379081-92539867	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv594861	chr4:92379081-92898309	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv948428	chr4:92382683-93161851	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv594862	chr4:92392152-93222515	Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv461585	chr4:92395356-92761582	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv594863	chr4:92395356-92761582	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv999961	chr4:92396538-93213898	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv537178	chr4:92396538-93213898	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
16	nsv533406	chr4:92396539-93184304	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv530154	chr4:92396539-93359983	Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv879585	chr4:92415529-92520419	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv879586	chr4:92432161-92520419	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	n/a	n/a	inside rSNPs	diseases
20	nsv879587	chr4:92432161-92539867	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv1011956	chr4:92473302-92506022	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
22	nsv1006366	chr4:92481747-92755677	Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
23	nsv1003269	chr4:92488825-92758977	Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1516708	ARHGEF10	trans	cerebellum	SCAN
rs1516708	HERC5	cis	parietal	SCAN
rs1516708	ABCG2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:92497600-92503000	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr4:92499800-92502400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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