Variant report

Variant	rs12613903
Chromosome Location	chr2:190352834-190352835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:190351757-190352948	T-47D	breast:	n/a	n/a
2	ESR1	chr2:190351716-190352959	T-47D	breast:	n/a	n/a
3	JUND	chr2:190351760-190353028	T-47D	breast:	n/a	n/a
4	CTCF	chr2:190352781-190352844	GM10266	blood:	n/a	n/a
5	FOXA1	chr2:190351834-190352990	T-47D	breast:	n/a	n/a
6	GATA3	chr2:190351736-190352937	T-47D	breast:	n/a	n/a
7	GATA3	chr2:190351876-190352848	MCF-7	breast:	n/a	n/a
8	FOXA1	chr2:190351742-190352922	T-47D	breast:	n/a	n/a
9	ESR1	chr2:190351808-190352850	T-47D	breast:	n/a	n/a
10	EP300	chr2:190352025-190352837	MCF-7	breast:	n/a	n/a
11	FOXA2	chr2:190352572-190352837	HepG2	liver:	n/a	n/a
12	ESR1	chr2:190351718-190352914	T-47D	breast:	n/a	n/a
13	ESR1	chr2:190351787-190352957	T-47D	breast:	n/a	n/a
14	GATA3	chr2:190351704-190352926	T-47D	breast:	n/a	n/a
15	GATA3	chr2:190351794-190352840	MCF-7	breast:	n/a	n/a
16	EP300	chr2:190351603-190352997	T-47D	breast:	n/a	n/a
17	ESR1	chr2:190351833-190352932	T-47D	breast:	n/a	n/a
18	ESR1	chr2:190351712-190352883	T-47D	breast:	n/a	n/a
19	JUND	chr2:190351758-190352955	T-47D	breast:	n/a	n/a

No data

Variant related genes	Relation type
ENSG00000233996	TF binding region

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

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

rs_ID	r²[population]
rs10166420	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10175108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.91[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];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12622720	1.00[ASN][1000 genomes]
rs12623394	0.93[ASN][1000 genomes]
rs12693539	0.91[ASN][1000 genomes]
rs12693540	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009912	0.93[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];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831454	0.81[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];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1866606	0.82[ASN][1000 genomes]
rs1898971	0.84[AFR][1000 genomes];0.97[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	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2351934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2882805	0.83[ASN][1000 genomes]
rs4309611	0.87[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];0.96[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];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6738193	0.91[ASN][1000 genomes]
rs6747222	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6752545	0.82[ASN][1000 genomes]
rs734859	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs744556	0.93[ASN][1000 genomes]
rs745742	0.90[AFR][1000 genomes];0.99[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]
rs893407	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs12613903	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190335000-190366200	Weak transcription	Ovary	ovary
2	chr2:190342400-190357000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:190349200-190365000	Weak transcription	Fetal Intestine Large	intestine
4	chr2:190350800-190353000	Enhancers	Liver	Liver
5	chr2:190351600-190353000	Enhancers	Placenta	Placenta
6	chr2:190352200-190353000	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr2:190352600-190353000	Enhancers	Rectal Smooth Muscle	rectum

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