Variant report

Variant	rs2956964
Chromosome Location	chr8:1570151-1570152
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154989909..154990782-chr8:1569714..1570480,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ERICH1-6	chr8:1569302-1570583	ENSG00000253267.1

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11777547	0.85[CEU][hapmap]
rs11786332	0.90[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11786502	0.82[CEU][hapmap]
rs13259879	0.90[CEU][hapmap];0.82[GIH][hapmap]
rs17828747	0.82[CEU][hapmap]
rs2956940	0.95[CEU][hapmap]
rs2956963	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2957072	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957073	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2957076	0.86[CEU][hapmap]
rs2957078	0.81[CEU][hapmap]
rs2957087	0.95[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2957088	0.86[CEU][hapmap]
rs2957089	0.81[CEU][hapmap]
rs2957090	1.00[ASW][hapmap];0.95[CEU][hapmap];0.92[GIH][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2957091	0.86[CEU][hapmap]
rs2977206	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2977209	0.81[CEU][hapmap]
rs2977210	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2977211	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs2977218	1.00[CEU][hapmap]
rs2977221	0.81[CEU][hapmap]
rs34951699	0.86[ASN][1000 genomes]
rs4384004	0.80[EUR][1000 genomes]
rs736316	0.84[CEU][hapmap]
rs7465114	0.95[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap]
rs7826897	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[MKK][hapmap]
rs878016	0.90[CEU][hapmap];0.91[MEX][hapmap]
rs9644258	0.90[CEU][hapmap]
rs9644312	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028487	chr8:674077-1642737	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv932163	chr8:977218-1628286	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1026673	chr8:1142469-1679673	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv889697	chr8:1238564-1861971	Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv609509	chr8:1301110-1589888	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1031375	chr8:1320657-1722050	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv427811	chr8:1400816-1676653	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1031784	chr8:1518671-1596773	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1024534	chr8:1532291-1583640	Enhancers Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv1029421	chr8:1535762-1583640	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv1026633	chr8:1537126-1583640	ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1018421	chr8:1537126-1600857	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1027685	chr8:1537126-1613464	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1018273	chr8:1537401-1583640	Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv1025125	chr8:1544425-1583640	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv1034963	chr8:1544425-1681781	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1029332	chr8:1561756-1587877	Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv1026034	chr8:1561756-1596773	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv1021658	chr8:1561756-1613464	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	nsv1015597	chr8:1563559-1684995	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv539296	chr8:1563559-1684995	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv889704	chr8:1563904-1965389	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
23	nsv1032176	chr8:1564933-1603085	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
24	nsv1032697	chr8:1564933-1613464	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2956964	ARHGEF10	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:1562800-1572600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr8:1567800-1570200	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr8:1569800-1570400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr8:1569800-1570400	Active TSS	Spleen	Spleen
5	chr8:1570000-1570400	Enhancers	H9 Cell Line	embryonic stem cell
6	chr8:1570000-1571400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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