Variant report

Variant	rs10179547
Chromosome Location	chr2:182682028-182682029
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:182681410..182683561-chr2:182690955..182693010,2	MCF-7	breast:
2	chr2:182674283..182676270-chr2:182679368..182682318,3	MCF-7	breast:
3	chr2:182679351..182682085-chr2:182754696..182756887,2	MCF-7	breast:
4	chr2:182676782..182679506-chr2:182680066..182682576,2	K562	blood:

Variant related genes	Relation type
ENSG00000260742	Chromatin interaction
ENSG00000138434	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165226	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10165936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10173114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10176061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10176613	1.00[CEU][hapmap]
rs10176757	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs10179363	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10182213	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10183527	0.80[AFR][1000 genomes]
rs10190772	0.89[YRI][hapmap]
rs10199645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10200243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10201303	1.00[CEU][hapmap]
rs10210215	1.00[CEU][hapmap]
rs10221891	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs1106013	0.96[ASN][1000 genomes]
rs11884097	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs11886921	0.86[AFR][1000 genomes]
rs11895376	0.89[YRI][hapmap]
rs11901603	0.86[AFR][1000 genomes]
rs11902910	0.90[AFR][1000 genomes]
rs12620859	0.82[EUR][1000 genomes]
rs13404156	1.00[CEU][hapmap]
rs13414894	0.86[AFR][1000 genomes]
rs13415272	0.87[AFR][1000 genomes]
rs13424337	0.87[AFR][1000 genomes]
rs13425734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428496	0.89[AFR][1000 genomes]
rs1343793	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1528024	1.00[CEU][hapmap]
rs1528025	1.00[CEU][hapmap]
rs1528027	1.00[CEU][hapmap]
rs16867498	1.00[CEU][hapmap]
rs16867500	0.82[JPT][hapmap]
rs16867509	1.00[CEU][hapmap]
rs1881158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037799	0.81[AFR][1000 genomes]
rs2059702	1.00[CEU][hapmap]
rs2288330	1.00[CEU][hapmap]
rs2303554	1.00[CEU][hapmap]
rs2368224	1.00[CEU][hapmap]
rs2368225	0.83[AFR][1000 genomes]
rs3731693	1.00[CEU][hapmap]
rs3815877	1.00[CEU][hapmap]
rs3815878	1.00[CEU][hapmap]
rs6433943	1.00[CEU][hapmap]
rs6707164	1.00[CEU][hapmap]
rs6720109	1.00[CEU][hapmap]
rs6720702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6730859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6735322	1.00[CEU][hapmap]
rs6736766	1.00[CEU][hapmap]
rs6748354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6751685	1.00[CEU][hapmap]
rs6754192	1.00[CEU][hapmap]
rs6754481	0.80[AFR][1000 genomes]
rs6755017	1.00[CEU][hapmap]
rs7557969	1.00[CEU][hapmap]
rs7562680	1.00[CEU][hapmap]
rs7567220	0.86[AFR][1000 genomes]
rs7580410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7603721	1.00[CEU][hapmap]
rs7608942	1.00[CEU][hapmap]
rs9288073	0.86[AFR][1000 genomes]
rs9288074	0.85[AFR][1000 genomes]
rs937297	0.96[ASN][1000 genomes]
rs950165	0.96[ASN][1000 genomes]
rs951542	0.85[AFR][1000 genomes]
rs951543	0.86[AFR][1000 genomes]
rs9807949	1.00[CEU][hapmap]
rs9808112	1.00[CEU][hapmap]
rs9808113	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1001558	chr2:182590009-182732738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv834478	chr2:182654811-182843201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10179547	LOC647288///LOC730587	trans	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182671200-182682600	Weak transcription	Fetal Stomach	stomach
2	chr2:182676200-182682600	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:182676800-182682400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:182676800-182686400	Weak transcription	Pancreas	Pancrea
5	chr2:182677200-182683600	Weak transcription	Fetal Kidney	kidney
6	chr2:182677600-182683600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:182679400-182682400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:182679400-182683400	Weak transcription	HUVEC	blood vessel
9	chr2:182680200-182683600	Weak transcription	Fetal Lung	lung
10	chr2:182680400-182683800	Weak transcription	Placenta	Placenta
11	chr2:182680400-182683800	Weak transcription	Fetal Thymus	thymus
12	chr2:182681200-182682200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:182681200-182683200	Enhancers	Hela-S3	cervix
14	chr2:182681200-182683800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:182681400-182682400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr2:182681800-182682600	Enhancers	NH-A	brain
17	chr2:182682000-182682200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:182682000-182682600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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