Variant report

Variant	rs10169022
Chromosome Location	chr2:112792656-112792657
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:112654547..112656932-chr2:112789072..112792767,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153208	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10176660	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10176769	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10192728	0.91[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10194496	0.82[JPT][hapmap]
rs10195619	0.81[CEU][hapmap]
rs10207301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10864895	0.85[CEU][hapmap]
rs1122970	0.82[CEU][hapmap]
rs11674226	0.82[CEU][hapmap]
rs11674883	0.82[CEU][hapmap]
rs11674891	0.82[CEU][hapmap]
rs11679125	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11679593	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11679801	0.81[CEU][hapmap]
rs11682629	0.82[CEU][hapmap]
rs11683694	0.82[CEU][hapmap]
rs11684321	0.85[CEU][hapmap];0.84[CHB][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap]
rs11684476	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11685190	0.82[CEU][hapmap]
rs11687451	0.82[CEU][hapmap]
rs11690440	0.85[ASN][1000 genomes]
rs11692445	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs11897014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12995767	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13001162	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13003919	0.82[CEU][hapmap]
rs13006228	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13020304	0.82[CEU][hapmap]
rs13024271	0.90[ASN][1000 genomes]
rs13027171	0.82[CEU][hapmap]
rs13033393	0.82[CEU][hapmap]
rs1554216	0.81[CEU][hapmap]
rs2271701	0.82[CEU][hapmap]
rs34128716	0.90[ASN][1000 genomes]
rs34240639	0.90[ASN][1000 genomes]
rs34593596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35643003	0.81[ASN][1000 genomes]
rs3761699	0.82[CEU][hapmap]
rs3811633	0.82[CEU][hapmap]
rs3811634	0.82[CEU][hapmap]
rs4575728	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4632347	0.82[JPT][hapmap]
rs4848229	0.82[CEU][hapmap]
rs4848238	0.82[CEU][hapmap]
rs4848874	0.82[CEU][hapmap]
rs4848958	0.81[ASN][1000 genomes]
rs4848971	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848973	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4848975	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4848979	0.91[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4848980	0.89[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6704665	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6722814	0.91[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743523	0.81[CEU][hapmap]
rs6748256	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs72829613	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586558	0.96[ASN][1000 genomes]
rs870761	0.81[CEU][hapmap]
rs870763	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv999746	chr2:112691270-112796083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv2760607	chr2:112691282-112803423	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv431491	chr2:112699350-112793981	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv515698	chr2:112699350-112795908	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv1793068	chr2:112784234-112816694	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv979100	chr2:112792445-112806085	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10169022	RANBP2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112783200-112802200	Weak transcription	Aorta	Aorta
2	chr2:112786200-112798800	Weak transcription	K562	blood
3	chr2:112786400-112796000	Weak transcription	Gastric	stomach
4	chr2:112790800-112799600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:112791000-112798800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:112791400-112794800	Weak transcription	Left Ventricle	heart
7	chr2:112791600-112797200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:112791600-112798800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:112792000-112794800	Weak transcription	Esophagus	oesophagus

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