Variant report

Variant	rs12504273
Chromosome Location	chr4:152549112-152549113
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	chr4:152547828..152549705-chr4:152551466..152554040,2	MCF-7	breast:

Extended variants
information (count: 144 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10001439	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs10009423	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs10025109	0.87[EUR][1000 genomes]
rs10031175	0.87[EUR][1000 genomes]
rs10857261	0.89[EUR][1000 genomes]
rs11099813	0.86[EUR][1000 genomes]
rs11099818	0.92[EUR][1000 genomes]
rs11099824	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11556167	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11723643	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11726171	0.86[EUR][1000 genomes]
rs11726222	0.92[EUR][1000 genomes]
rs11726545	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728541	0.84[EUR][1000 genomes]
rs11729514	0.92[EUR][1000 genomes]
rs11729871	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11730733	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11732441	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs11732453	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11734176	0.84[EUR][1000 genomes]
rs11735143	0.92[EUR][1000 genomes]
rs11736261	0.84[EUR][1000 genomes]
rs11736961	0.92[EUR][1000 genomes]
rs11934818	0.92[EUR][1000 genomes]
rs11947720	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12054502	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12498556	0.92[EUR][1000 genomes]
rs12498878	0.92[EUR][1000 genomes]
rs12502212	0.92[EUR][1000 genomes]
rs12502967	0.84[EUR][1000 genomes]
rs12508678	0.92[EUR][1000 genomes]
rs12511280	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1366908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1366910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1372979	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1443085	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17027716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17027818	0.84[EUR][1000 genomes]
rs17275584	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17275605	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17275612	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17360294	0.89[CEU][hapmap]
rs17360378	0.89[CEU][hapmap]
rs1992517	0.92[EUR][1000 genomes]
rs2406972	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs28417319	0.84[EUR][1000 genomes]
rs28447105	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28463438	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28483174	0.87[EUR][1000 genomes]
rs28498882	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28527216	0.87[EUR][1000 genomes]
rs28545583	0.87[EUR][1000 genomes]
rs28574706	0.87[EUR][1000 genomes]
rs28605105	0.84[EUR][1000 genomes]
rs28608075	0.84[EUR][1000 genomes]
rs28608757	0.84[EUR][1000 genomes]
rs28672085	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28706249	0.84[EUR][1000 genomes]
rs28715753	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3172567	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35588363	0.84[EUR][1000 genomes]
rs36083376	0.92[EUR][1000 genomes]
rs3762906	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs3792689	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3811748	0.84[EUR][1000 genomes]
rs3811749	0.84[EUR][1000 genomes]
rs3934474	0.92[EUR][1000 genomes]
rs4371601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4385035	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4622982	0.90[EUR][1000 genomes]
rs56092201	0.92[EUR][1000 genomes]
rs56199243	0.83[EUR][1000 genomes]
rs56763519	0.89[EUR][1000 genomes]
rs57272881	0.92[EUR][1000 genomes]
rs57348790	0.85[EUR][1000 genomes]
rs57556564	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58443173	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58961701	0.87[EUR][1000 genomes]
rs59731141	0.92[EUR][1000 genomes]
rs59744221	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59777523	0.84[EUR][1000 genomes]
rs59811197	0.90[EUR][1000 genomes]
rs59984665	0.92[EUR][1000 genomes]
rs60055392	0.84[EUR][1000 genomes]
rs60077220	0.92[EUR][1000 genomes]
rs60122169	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60169090	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60618075	0.88[EUR][1000 genomes]
rs60707008	0.92[EUR][1000 genomes]
rs61294884	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61302767	0.92[EUR][1000 genomes]
rs61630225	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6535802	0.92[EUR][1000 genomes]
rs6535805	0.90[CEU][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6812000	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6813289	0.84[EUR][1000 genomes]
rs6817373	0.87[EUR][1000 genomes]
rs6822729	0.87[EUR][1000 genomes]
rs6822737	0.84[EUR][1000 genomes]
rs6826318	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832899	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6832902	0.84[EUR][1000 genomes]
rs6833277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6835310	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838608	0.90[EUR][1000 genomes]
rs6839738	0.94[EUR][1000 genomes]
rs6841515	0.84[EUR][1000 genomes]
rs6843267	0.87[EUR][1000 genomes]
rs6844169	0.92[EUR][1000 genomes]
rs6845067	0.92[EUR][1000 genomes]
rs6846013	0.92[EUR][1000 genomes]
rs6846759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6851305	0.84[EUR][1000 genomes]
rs6853342	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856392	0.87[EUR][1000 genomes]
rs6858573	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72962929	0.84[EUR][1000 genomes]
rs72964908	0.84[AMR][1000 genomes]
rs73861275	0.84[EUR][1000 genomes]
rs73861826	0.89[EUR][1000 genomes]
rs73861827	0.89[EUR][1000 genomes]
rs73862055	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73862076	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73862080	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73862085	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73864013	0.89[EUR][1000 genomes]
rs7438281	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7653926	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7655466	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662214	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7662713	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664074	0.92[EUR][1000 genomes]
rs7671456	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7675933	0.84[EUR][1000 genomes]
rs7677528	1.00[CEU][hapmap];0.81[CHB][hapmap];0.92[EUR][1000 genomes]
rs7690773	0.84[EUR][1000 genomes]
rs7696468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs7699787	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9683881	0.86[EUR][1000 genomes]
rs9917912	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9996600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs9999456	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880624	chr4:152280646-152549112	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv881342	chr4:152363772-152560449	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12504273	FAM160A1	cis	cerebellum	SCAN
rs12504273	LRBA	cis	cerebellum	SCAN
rs12504273	SH3D19	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152499200-152567600	Weak transcription	Pancreas	Pancrea
2	chr4:152522400-152560200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:152542400-152565600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:152544000-152570600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr4:152544200-152566400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr4:152544400-152570600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152545400-152549200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr4:152545600-152578600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr4:152546000-152550800	Weak transcription	Lung	lung
10	chr4:152546400-152550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:152546400-152552800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:152546400-152561800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:152546400-152570600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:152547400-152550600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:152548200-152558800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:152548400-152549200	Enhancers	HMEC	breast
17	chr4:152548400-152549200	Enhancers	NHEK	skin
18	chr4:152548400-152549400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:152548400-152549400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:152548400-152549600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:152548400-152550200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr4:152548600-152549200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:152548600-152550000	Enhancers	NHDF-Ad	bronchial
24	chr4:152548800-152558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:152549000-152549200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:152549000-152549600	Enhancers	Fetal Heart	heart
27	chr4:152549000-152567000	Weak transcription	Rectal Mucosa Donor 29	rectum

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