Variant report

Variant	rs12257639
Chromosome Location	chr10:98048614-98048615
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:97889408..97891756-chr10:98048251..98051356,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177853	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10509707	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10882767	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10882768	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11188699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12250473	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12411820	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12414495	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12414529	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12572610	0.90[EUR][1000 genomes]
rs17111536	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17111540	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2069238	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2146391	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3762093	0.83[AMR][1000 genomes]
rs3789933	0.82[AMR][1000 genomes]
rs3789939	0.82[AMR][1000 genomes]
rs41291614	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4917730	0.85[ASN][1000 genomes]
rs57519557	0.94[AMR][1000 genomes]
rs6584064	0.87[ASN][1000 genomes]
rs67425977	0.87[AMR][1000 genomes]
rs7069190	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7072251	0.86[ASN][1000 genomes]
rs7074775	0.82[AMR][1000 genomes]
rs7078316	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7083595	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7091809	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72637514	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72637515	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72637516	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72640001	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7896766	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7905402	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7919557	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7919588	0.85[ASN][1000 genomes]
rs7919799	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7922788	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941998	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941999	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	esv3413353	chr10:98039370-98561524	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	esv2761620	chr10:98047045-98089749	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98045600-98049800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:98045600-98052800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr10:98045600-98053000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr10:98046600-98050800	Enhancers	Fetal Thymus	thymus
5	chr10:98046800-98049400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr10:98047000-98050400	Enhancers	Placenta	Placenta
7	chr10:98047200-98048800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr10:98047600-98048800	Enhancers	Duodenum Mucosa	Duodenum
9	chr10:98048200-98049000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:98048200-98050200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr10:98048200-98050200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:98048200-98050400	Enhancers	Thymus	Thymus
13	chr10:98048200-98052800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr10:98048200-98053000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:98048400-98049200	Enhancers	Fetal Intestine Large	intestine
16	chr10:98048400-98049800	Weak transcription	Fetal Kidney	kidney
17	chr10:98048400-98050800	Enhancers	Fetal Intestine Small	intestine
18	chr10:98048400-98052800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:98048400-98053200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr10:98048400-98053600	Enhancers	Primary B cells from peripheral blood	blood
21	chr10:98048600-98049200	Enhancers	GM12878-XiMat	blood
22	chr10:98048600-98049400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:98048600-98049800	Enhancers	Primary B cells from cord blood	blood
24	chr10:98048600-98050400	Weak transcription	Dnd41	blood
25	chr10:98048600-98053400	Weak transcription	Liver	Liver
26	chr10:98048600-98058800	Weak transcription	Primary hematopoietic stem cells	blood

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