Variant report

Variant	rs1872239
Chromosome Location	chr3:136503911-136503912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136503077..136505635-chr3:136505937..136507596,2	MCF-7	breast:
2	chr3:136502917..136505188-chr3:136511396..136514165,2	MCF-7	breast:
3	chr3:136498020..136500935-chr3:136501120..136504401,3	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1052620	0.93[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs12695649	1.00[ASN][1000 genomes]
rs13062352	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13066401	1.00[ASN][1000 genomes]
rs13071220	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs13080786	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100192	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13314357	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326151	1.00[ASN][1000 genomes]
rs13433683	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433688	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434116	1.00[ASN][1000 genomes]
rs17365792	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176269	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370972	1.00[ASN][1000 genomes]
rs28390205	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28472992	1.00[ASN][1000 genomes]
rs28489326	1.00[ASN][1000 genomes]
rs28641809	1.00[ASN][1000 genomes]
rs28750366	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs28877020	1.00[ASN][1000 genomes]
rs34564818	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34645606	1.00[ASN][1000 genomes]
rs34804893	0.86[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34969907	1.00[ASN][1000 genomes]
rs35096613	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35100027	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35198484	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35210994	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35422852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35428413	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880395	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36109616	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36177165	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4038586	0.93[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs4470449	1.00[ASN][1000 genomes]
rs66509730	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67145204	1.00[ASN][1000 genomes]
rs67382287	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767889	1.00[ASN][1000 genomes]
rs6774964	1.00[ASN][1000 genomes]
rs6806123	0.93[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];1.00[ASN][1000 genomes]
rs71310215	0.81[AMR][1000 genomes]
rs71336069	1.00[ASN][1000 genomes]
rs71336080	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230043	1.00[ASN][1000 genomes]
rs73230099	1.00[ASN][1000 genomes]
rs73231903	1.00[ASN][1000 genomes]
rs9289513	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9809269	1.00[ASN][1000 genomes]
rs9809988	0.93[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813376	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9813691	1.00[ASN][1000 genomes]
rs9819856	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820717	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828976	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840500	1.00[ASN][1000 genomes]
rs9845862	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847427	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850364	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857833	1.00[ASN][1000 genomes]
rs9857966	1.00[ASN][1000 genomes]
rs9858560	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860879	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865995	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867325	0.93[CEU][hapmap];1.00[ASN][1000 genomes]
rs9871184	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873536	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875770	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879531	1.00[ASN][1000 genomes]
rs9881831	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883189	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006737	chr3:136466188-136530743	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1872239	ERICH1	trans	parietal	SCAN
rs1872239	RNF184	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136498200-136504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:136498200-136505000	Weak transcription	Osteobl	bone
3	chr3:136498200-136505800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:136499200-136504400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:136500000-136505400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:136500200-136508000	Enhancers	Placenta	Placenta
7	chr3:136502400-136504600	Enhancers	A549	lung
8	chr3:136502800-136504000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:136502800-136504000	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:136502800-136504400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:136502800-136504600	Weak transcription	Right Atrium	heart
12	chr3:136502800-136504800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:136502800-136505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:136502800-136505000	Weak transcription	Fetal Lung	lung
15	chr3:136502800-136505000	Weak transcription	Fetal Stomach	stomach
16	chr3:136502800-136505000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:136502800-136505000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:136502800-136505000	Enhancers	Hela-S3	cervix
19	chr3:136503000-136504400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:136503000-136504400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:136503000-136504600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:136503000-136505000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr3:136503000-136505000	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:136503000-136505000	Weak transcription	HSMM	muscle
25	chr3:136503000-136505200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:136503000-136505200	Weak transcription	HSMMtube	muscle
27	chr3:136503000-136505200	Weak transcription	NH-A	brain
28	chr3:136503000-136505400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:136503200-136504600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:136503200-136505000	Weak transcription	Fetal Thymus	thymus
31	chr3:136503800-136504600	Weak transcription	Aorta	Aorta
32	chr3:136503800-136505200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:136503800-136505200	Enhancers	NHLF	lung

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