Variant report

Variant	rs1872240
Chromosome Location	chr3:136503896-136503897
allele	A/G
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: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10155016	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155017	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513014	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs10513016	1.00[CHB][hapmap]
rs13433980	1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs1484250	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17365351	1.00[CHB][hapmap]
rs17466223	1.00[CHB][hapmap]
rs28682370	0.82[EUR][1000 genomes]
rs34992220	0.86[CEU][hapmap];0.93[MEX][hapmap]
rs4336059	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs6763239	0.82[EUR][1000 genomes]
rs6765239	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6771713	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6772759	0.82[EUR][1000 genomes]
rs6782151	0.95[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap]
rs6789329	0.91[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.83[EUR][1000 genomes]
rs6799699	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs6800969	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs7623824	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs7626418	0.82[EUR][1000 genomes]
rs7629905	0.81[EUR][1000 genomes]
rs7644346	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs7646563	1.00[CHB][hapmap]
rs7646723	1.00[CHB][hapmap]
rs923001	1.00[CHB][hapmap]
rs9818372	0.82[EUR][1000 genomes]
rs9820513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9828068	0.81[EUR][1000 genomes]
rs9839574	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap]
rs9845950	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs9853960	0.83[EUR][1000 genomes]
rs9869361	0.81[EUR][1000 genomes]
rs9869957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs9881078	0.98[EUR][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
rs1872240	RNF184	cis	multi-tissue	Pritchard
rs1872240	SCN9A	trans	cerebellum	SCAN

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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