Variant report

Variant	rs5024546
Chromosome Location	chr10:27988298-27988299
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	chr10:27987243..27989014-chr10:28013430..28015177,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10826347	0.86[CEU][hapmap]
rs10829311	0.86[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11006695	0.86[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11006701	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11015956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11015961	0.86[CEU][hapmap]
rs11015964	0.86[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11015965	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11015966	0.86[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12217587	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12217663	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12257885	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12258832	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16928202	0.93[CEU][hapmap]
rs1907374	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs1907390	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1907391	1.00[ASN][1000 genomes]
rs1907392	0.82[CEU][hapmap]
rs2246903	1.00[ASN][1000 genomes]
rs2368249	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2368250	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2451915	1.00[ASN][1000 genomes]
rs2451916	1.00[ASN][1000 genomes]
rs2451917	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2451919	0.98[ASN][1000 genomes]
rs2451920	1.00[ASN][1000 genomes]
rs2492912	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs2492913	1.00[ASN][1000 genomes]
rs2492914	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2492915	1.00[ASN][1000 genomes]
rs2492916	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2492917	0.98[ASN][1000 genomes]
rs2637303	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs2637304	0.98[ASN][1000 genomes]
rs2637328	1.00[ASN][1000 genomes]
rs2815560	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[ASN][1000 genomes]
rs2815561	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2815562	1.00[ASN][1000 genomes]
rs2815563	0.96[ASN][1000 genomes]
rs2815565	1.00[ASN][1000 genomes]
rs2815567	0.85[ASN][1000 genomes]
rs2815569	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2815570	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2815571	1.00[ASN][1000 genomes]
rs2815573	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2815574	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815575	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815576	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2815577	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2999980	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4417171	0.86[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72799605	0.85[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	nsv550241	chr10:27569521-28025771	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3368825	chr10:27864181-28043820	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27982400-27988800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr10:27984400-27990800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:27984400-27990800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:27984600-27989200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr10:27985400-27988600	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:27985400-27990800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:27985600-27988400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr10:27985800-27988400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:27985800-27990800	Weak transcription	Osteobl	bone
10	chr10:27985800-28001400	Weak transcription	Aorta	Aorta
11	chr10:27986800-27989400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr10:27987000-27988600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:27987200-27989600	Enhancers	Fetal Stomach	stomach
14	chr10:27987400-27990800	Weak transcription	Fetal Muscle Leg	muscle
15	chr10:27987600-27988600	Weak transcription	Ovary	ovary
16	chr10:27988200-27990400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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