Variant report

Variant	rs10201153
Chromosome Location	chr2:178440641-178440642
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	chr2:178431853..178433434-chr2:178438526..178441127,2	MCF-7	breast:
2	chr2:178415755..178417971-chr2:178438739..178440654,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196659	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10170546	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10170667	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs10196345	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10497500	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs10497501	0.82[JPT][hapmap]
rs10497502	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs10497503	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs10497508	0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs12469386	0.85[JPT][hapmap]
rs12612857	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12615367	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs12616093	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12618139	0.85[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs13000048	0.85[JPT][hapmap]
rs13004955	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13403787	0.84[ASN][1000 genomes]
rs13404970	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13417231	0.87[ASN][1000 genomes]
rs13430517	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1348848	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1348849	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1348850	0.95[JPT][hapmap]
rs1374437	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1405713	0.86[JPT][hapmap]
rs1453370	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1548067	0.86[JPT][hapmap]
rs16865203	0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs16865291	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs16865328	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs16865331	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16865433	0.97[EUR][1000 genomes]
rs2060929	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2084233	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs2121430	0.85[JPT][hapmap]
rs2166558	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs2364854	0.85[JPT][hapmap]
rs3213945	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769995	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3769996	0.85[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs3769997	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs3770002	0.90[JPT][hapmap]
rs3813259	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4243388	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs4528793	0.86[JPT][hapmap]
rs4893822	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs4893823	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs4893825	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs4893936	0.84[JPT][hapmap]
rs4893950	0.84[JPT][hapmap]
rs4893957	0.81[CHB][hapmap]
rs4893959	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs4893961	0.95[JPT][hapmap]
rs4893962	0.95[JPT][hapmap]
rs4893965	0.86[JPT][hapmap]
rs57562172	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59666005	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60642012	0.82[EUR][1000 genomes]
rs6710575	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs6717572	0.82[EUR][1000 genomes]
rs6742951	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7587604	0.85[JPT][hapmap]
rs7591807	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7604673	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7606235	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs8941	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs9288004	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9288005	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs952746	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10201153	LOC100130691	cis	lymphoblastoid	seeQTL
rs10201153		cis	Lymphoblastoid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178438000-178449800	Weak transcription	Pancreas	Pancrea
2	chr2:178438200-178443600	Weak transcription	HepG2	liver
3	chr2:178440200-178440800	Enhancers	Colon Smooth Muscle	Colon
4	chr2:178440200-178443200	Weak transcription	Fetal Heart	heart

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