Variant report

Variant	rs893407
Chromosome Location	chr2:190350534-190350535
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	chr2:190347309..190351333-chr2:190419513..190421740,3	MCF-7	breast:
2	chr2:190349773..190352043-chr2:190405227..190407420,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10166420	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10175108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs10210634	0.82[ASN][1000 genomes]
rs10931417	0.82[ASN][1000 genomes]
rs11677167	0.82[ASN][1000 genomes]
rs11678414	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12613903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622720	1.00[ASN][1000 genomes]
rs12623394	0.93[ASN][1000 genomes]
rs12693539	0.91[ASN][1000 genomes]
rs12693540	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009912	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13015207	0.91[ASN][1000 genomes]
rs13018252	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs13035381	0.82[ASN][1000 genomes]
rs1356976	0.83[ASN][1000 genomes]
rs1520854	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1520856	0.83[ASN][1000 genomes]
rs1520858	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1520866	0.94[ASN][1000 genomes]
rs1595749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831454	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1851104	1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1866605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1866606	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1898971	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992295	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2304702	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2351934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2882805	0.83[ASN][1000 genomes]
rs4309611	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4666775	0.94[ASN][1000 genomes]
rs4667280	0.80[ASN][1000 genomes]
rs4667284	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6434342	0.87[ASN][1000 genomes]
rs6434343	1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6738193	0.91[ASN][1000 genomes]
rs6747222	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6752545	0.82[ASN][1000 genomes]
rs734859	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs744556	0.93[ASN][1000 genomes]
rs745742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556928	0.82[ASN][1000 genomes]
rs7566093	0.82[ASN][1000 genomes]
rs7574403	0.91[ASN][1000 genomes]
rs8179541	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs893408	0.93[ASN][1000 genomes]
rs9677436	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs893407	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190351800	Weak transcription	Psoas Muscle	Psoas
2	chr2:190335000-190366200	Weak transcription	Ovary	ovary
3	chr2:190335800-190352600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr2:190339600-190352600	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:190340800-190352400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:190341600-190350800	Weak transcription	Liver	Liver
7	chr2:190341800-190351000	Weak transcription	HMEC	breast
8	chr2:190341800-190351200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
11	chr2:190349600-190351400	Enhancers	HSMMtube	muscle
12	chr2:190349600-190351600	Weak transcription	Placenta	Placenta
13	chr2:190350000-190351000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:190350000-190351600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:190350000-190352200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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