Variant report

Variant	rs4391505
Chromosome Location	chr9:85602289-85602290
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	chr9:85599966..85602793-chr9:85606688..85608759,2	MCF-7	breast:
2	chr9:85594172..85597684-chr9:85598731..85602466,4	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1008171	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1010480	0.89[CEU][hapmap]
rs10115768	0.84[EUR][1000 genomes]
rs10116216	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs10116254	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs10121204	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs10121376	0.87[EUR][1000 genomes]
rs10121395	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs10126033	0.82[EUR][1000 genomes]
rs10735559	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10746694	0.83[EUR][1000 genomes]
rs10780561	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10780562	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780563	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs10780564	0.91[EUR][1000 genomes]
rs10780565	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10780567	0.89[CEU][hapmap];0.81[GIH][hapmap];0.89[TSI][hapmap]
rs10867928	0.89[CEU][hapmap]
rs10867929	0.89[CEU][hapmap]
rs10867930	0.89[CEU][hapmap]
rs1125915	0.92[CEU][hapmap]
rs13302349	0.82[EUR][1000 genomes]
rs1393562	0.89[CEU][hapmap]
rs1393563	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1393564	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1393565	0.89[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1502682	0.89[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs1502683	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1502684	1.00[CEU][hapmap];0.89[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1502685	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs1546315	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs1546316	0.89[CEU][hapmap]
rs1546317	0.89[CEU][hapmap]
rs1580881	0.89[CEU][hapmap]
rs1976455	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs1995423	0.88[CEU][hapmap]
rs2062761	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2279814	0.89[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4146960	0.88[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs4146961	0.89[CEU][hapmap]
rs4301515	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4348583	0.85[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4355855	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4385545	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4460464	0.85[CEU][hapmap];0.86[GIH][hapmap]
rs4623517	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4877244	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs4877724	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877725	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4877726	0.88[CEU][hapmap]
rs6559693	0.87[EUR][1000 genomes]
rs6559694	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs6559695	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7019227	0.89[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs7024864	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7847666	0.88[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs7849126	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7853052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7854101	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs7862012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7864688	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7866666	0.89[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs7872982	0.81[EUR][1000 genomes]
rs871512	0.88[CEU][hapmap]
rs952450	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs998119	0.85[EUR][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	nsv1050771	chr9:85416931-85643417	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv6585	chr9:85566659-85611489	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4391505	RASEF	cis	multi-tissue	Pritchard
rs4391505	ATG2A	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85591200-85602800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:85592400-85602400	Weak transcription	Esophagus	oesophagus
3	chr9:85592800-85608600	Weak transcription	Stomach Mucosa	stomach
4	chr9:85594400-85602800	Weak transcription	Gastric	stomach
5	chr9:85594600-85606000	Weak transcription	Fetal Intestine Large	intestine
6	chr9:85594800-85628200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:85596200-85602400	Weak transcription	Fetal Stomach	stomach
8	chr9:85597200-85627000	Weak transcription	A549	lung
9	chr9:85597600-85608600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr9:85597600-85608600	Weak transcription	HMEC	breast
11	chr9:85600800-85604200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr9:85601200-85602800	Weak transcription	Pancreas	Pancrea
13	chr9:85601600-85603400	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr9:85601800-85603000	Enhancers	Fetal Intestine Small	intestine
15	chr9:85601800-85604400	Enhancers	Rectal Mucosa Donor 31	rectum

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