Variant report

Variant	rs17461231
Chromosome Location	chr1:113994893-113994894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113935271..113938235-chr1:113994077..113995754,2	MCF-7	breast:
2	chr1:113931751..113937304-chr1:113991927..113997733,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11102629	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11102646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11578447	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11579386	0.87[CEU][hapmap]
rs12117465	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs12117919	0.93[EUR][1000 genomes]
rs12119281	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125741	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12127683	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12130729	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12130763	1.00[EUR][1000 genomes]
rs12131115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12134802	0.89[EUR][1000 genomes]
rs12135714	0.89[EUR][1000 genomes]
rs12144505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs12145834	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17031376	1.00[ASN][1000 genomes]
rs17031640	0.87[CEU][hapmap]
rs17031645	0.87[CEU][hapmap]
rs17031648	0.87[CEU][hapmap]
rs17448063	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs17461007	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17507884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[EUR][1000 genomes]
rs1936931	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2359415	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55710846	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61817493	1.00[ASN][1000 genomes]
rs6537788	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671518	0.87[CEU][hapmap]
rs6696459	0.87[CEU][hapmap]
rs7514186	0.87[CEU][hapmap]
rs7528311	0.87[CEU][hapmap]
rs7533429	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7555259	0.87[CEU][hapmap]

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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113985000-113999000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr1:113987800-113996000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:113994200-113995000	Enhancers	Colon Smooth Muscle	Colon
4	chr1:113994200-113995000	Enhancers	Duodenum Mucosa	Duodenum
5	chr1:113994200-113995000	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr1:113994200-113995000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr1:113994200-113995400	Enhancers	Stomach Mucosa	stomach
8	chr1:113994200-113996400	Enhancers	HUVEC	blood vessel
9	chr1:113994400-113995000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:113994400-113995000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:113994400-113995200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:113994400-113995200	Enhancers	Adipose Nuclei	Adipose
13	chr1:113994400-113996600	Enhancers	Liver	Liver
14	chr1:113994400-113996600	Enhancers	A549	lung
15	chr1:113994600-113995000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:113994600-113995000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr1:113994600-113995000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:113994600-113995400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:113994600-113995400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:113994600-113995400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr1:113994600-113995400	Weak transcription	Hela-S3	cervix
22	chr1:113994600-113995600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:113994600-113996600	Enhancers	Small Intestine	intestine
24	chr1:113994800-114004400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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