Variant report

Variant	rs6821624
Chromosome Location	chr4:92533513-92533514
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10009859	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap]
rs1003265	0.83[EUR][1000 genomes]
rs10470940	0.80[ASN][1000 genomes]
rs10516897	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1113135	0.83[ASN][1000 genomes]
rs1114290	0.84[JPT][hapmap]
rs1114625	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11723903	0.83[ASN][1000 genomes]
rs11932823	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs11940909	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11941818	0.83[EUR][1000 genomes]
rs11945625	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11946091	0.83[EUR][1000 genomes]
rs11947273	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12152593	0.84[JPT][hapmap]
rs12501164	0.82[EUR][1000 genomes]
rs13110767	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13111521	0.80[ASN][1000 genomes]
rs13117758	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13134406	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13135264	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13135497	0.87[ASN][1000 genomes]
rs13149286	0.82[ASN][1000 genomes]
rs1356289	0.83[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs1400351	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1400352	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs1400353	0.83[JPT][hapmap]
rs1516699	0.86[GIH][hapmap];0.83[JPT][hapmap]
rs1516701	0.81[ASN][1000 genomes]
rs1516705	0.83[ASN][1000 genomes]
rs1516708	0.85[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs1568109	0.86[ASN][1000 genomes]
rs1588986	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs1914236	0.80[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs1914237	0.83[CHB][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1914238	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1914239	0.83[EUR][1000 genomes]
rs1914240	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2048867	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs2138581	0.83[JPT][hapmap]
rs35531607	0.81[ASN][1000 genomes]
rs4348056	0.84[ASN][1000 genomes]
rs4376107	0.81[ASN][1000 genomes]
rs4472103	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57015636	0.86[ASN][1000 genomes]
rs61143842	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6532317	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6532318	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs6532319	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs6532320	0.83[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs6532321	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6532322	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6532326	0.89[ASN][1000 genomes]
rs6532332	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6532334	0.81[EUR][1000 genomes]
rs6532335	0.82[EUR][1000 genomes]
rs6829570	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6834624	0.83[ASN][1000 genomes]
rs6845243	0.81[ASN][1000 genomes]
rs6852056	0.88[GIH][hapmap];0.83[JPT][hapmap]
rs7664136	0.87[ASN][1000 genomes]
rs7667244	0.84[JPT][hapmap]
rs7669292	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7670997	0.83[ASN][1000 genomes]
rs7675352	0.80[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs7676835	0.83[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap]
rs7681874	0.83[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs7687544	0.80[ASN][1000 genomes]
rs7693738	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs7696964	0.83[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs868796	0.81[ASN][1000 genomes]
rs955009	0.80[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9997172	0.83[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	nsv869490	chr4:92506402-93219336	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv999701	chr4:92518040-93233556	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv537180	chr4:92518040-93233556	Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
20	nsv530442	chr4:92528849-93184304	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6821624	ABCG2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:92532600-92533600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:92532600-92533800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr4:92532800-92533600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:92533200-92534200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:92533400-92543600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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