Variant report

Variant	rs12264840
Chromosome Location	chr10:90711301-90711302
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	chr10:90694957..90695602-chr10:90711260..90711824,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10509558	0.91[CHB][hapmap]
rs10509559	0.91[CHB][hapmap]
rs10509560	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10887870	0.92[ASN][1000 genomes]
rs11202875	1.00[CEU][hapmap]
rs11202906	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs11202907	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12242191	1.00[CEU][hapmap]
rs12242274	0.91[CHB][hapmap]
rs12243282	0.91[CHB][hapmap]
rs12243621	0.91[CHB][hapmap]
rs12247227	0.88[CHB][hapmap]
rs12260572	0.91[CHB][hapmap]
rs12262461	0.91[CHB][hapmap]
rs17096285	1.00[CEU][hapmap]
rs17113942	0.91[CHB][hapmap]
rs17113959	0.91[CHB][hapmap]
rs17114000	0.91[CHB][hapmap]
rs17114016	0.91[CHB][hapmap]
rs17114020	0.91[CHB][hapmap]
rs17114024	0.91[CHB][hapmap]
rs17114057	0.91[CHB][hapmap]
rs17114116	1.00[CHB][hapmap]
rs17114120	1.00[CEU][hapmap]
rs17114143	1.00[CHB][hapmap]
rs17114186	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17114283	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs17114327	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2119685	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs2147416	1.00[CEU][hapmap]
rs2231780	0.91[CHB][hapmap]
rs2231785	0.91[CHB][hapmap]
rs2231786	0.91[CHB][hapmap]
rs3758487	1.00[CEU][hapmap]
rs3781206	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs3781208	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3781212	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816245	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs3898173	0.91[CHB][hapmap]
rs3898174	0.91[CHB][hapmap]
rs7070713	1.00[CHB][hapmap]
rs7077534	1.00[CEU][hapmap]
rs7077956	1.00[CEU][hapmap]
rs7078383	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[ASN][1000 genomes]
rs7085698	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7090631	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs7098235	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs74147448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7897521	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7899463	1.00[CEU][hapmap]
rs7908852	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs7911566	1.00[CEU][hapmap]
rs7915393	1.00[CHB][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv831943	chr10:90664836-90865834	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90695800-90720800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr10:90699000-90724200	Weak transcription	Small Intestine	intestine
3	chr10:90699400-90715400	Weak transcription	HepG2	liver
4	chr10:90699600-90712200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:90699600-90721800	Weak transcription	Fetal Thymus	thymus
6	chr10:90700000-90712000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr10:90701400-90720800	Weak transcription	Primary T cells from cord blood	blood
8	chr10:90701600-90711600	Weak transcription	Esophagus	oesophagus
9	chr10:90703600-90711600	Weak transcription	Spleen	Spleen
10	chr10:90703800-90711600	Weak transcription	Pancreas	Pancrea
11	chr10:90704000-90711600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr10:90704000-90721400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr10:90705000-90721800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr10:90705800-90712800	Weak transcription	Primary B cells from cord blood	blood
15	chr10:90707000-90713200	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr10:90707200-90711400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr10:90707800-90712400	Active TSS	HSMMtube	muscle
18	chr10:90708400-90713000	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr10:90708600-90712400	Active TSS	Fetal Intestine Large	intestine
20	chr10:90708800-90712800	Active TSS	Fetal Intestine Small	intestine
21	chr10:90708800-90713600	Active TSS	Stomach Smooth Muscle	stomach
22	chr10:90709000-90712200	Active TSS	Colon Smooth Muscle	Colon
23	chr10:90709000-90713200	Active TSS	Aorta	Aorta
24	chr10:90709200-90712800	Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr10:90709600-90713000	Flanking Active TSS	Osteobl	bone
26	chr10:90709800-90711400	Flanking Active TSS	NHDF-Ad	bronchial
27	chr10:90709800-90712200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:90709800-90712400	Active TSS	Duodenum Mucosa	Duodenum
29	chr10:90709800-90712800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:90710000-90711400	Active TSS	Right Atrium	heart
31	chr10:90710000-90711600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr10:90710000-90712200	Active TSS	Colonic Mucosa	Colon
33	chr10:90710000-90712400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:90710000-90712400	Active TSS	Right Ventricle	heart
35	chr10:90710000-90712800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr10:90710000-90713000	Active TSS	Ovary	ovary
37	chr10:90710200-90711400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:90710200-90711400	Enhancers	Brain Anterior Caudate	brain
39	chr10:90710200-90712400	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr10:90710200-90712400	Active TSS	Psoas Muscle	Psoas
41	chr10:90710200-90712800	Flanking Active TSS	HSMM	muscle
42	chr10:90710200-90713000	Flanking Active TSS	Fetal Lung	lung
43	chr10:90710400-90711400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr10:90710400-90711600	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr10:90710400-90712400	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr10:90710400-90713000	Flanking Active TSS	Fetal Heart	heart
47	chr10:90710600-90711800	Flanking Active TSS	NH-A	brain
48	chr10:90710600-90712000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:90710600-90712200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr10:90710800-90711400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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