Variant report

Variant	rs11254828
Chromosome Location	chr10:5764481-5764482
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:5730140..5732838-chr10:5762555..5765263,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11253740	1.00[CEU][hapmap]
rs11254115	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11254891	1.00[CEU][hapmap]
rs11254898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12257412	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12263390	1.00[CEU][hapmap]
rs12263869	1.00[CEU][hapmap]
rs12269174	1.00[CEU][hapmap]
rs12571055	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12572339	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1567708	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2246268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275772	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2380197	1.00[CEU][hapmap]
rs2669133	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2669139	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797490	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797497	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34404996	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3750636	0.90[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3793708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793714	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs3924378	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs57103262	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58502403	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59827083	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7089693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7096328	0.93[ASN][1000 genomes]
rs73610559	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7893673	0.89[AMR][1000 genomes]
rs7908235	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534685	chr10:4914018-5853324	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2759729	chr10:5557024-5804780	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv2758209	chr10:5637111-5804780	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv1796213	chr10:5716555-5766165	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv522415	chr10:5721653-5768493	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv34147	chr10:5726821-6105717	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv1050663	chr10:5737979-5785918	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv519891	chr10:5753737-5768493	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv525080	chr10:5754611-5766337	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5735200-5767000	Weak transcription	Fetal Muscle Leg	muscle
2	chr10:5738600-5769000	Weak transcription	Left Ventricle	heart
3	chr10:5740400-5768600	Weak transcription	Psoas Muscle	Psoas
4	chr10:5741400-5765600	Weak transcription	A549	lung
5	chr10:5752600-5767000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr10:5753800-5764600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr10:5753800-5765600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr10:5753800-5768600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr10:5753800-5769000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr10:5753800-5769000	Weak transcription	Thymus	Thymus
11	chr10:5753800-5772200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr10:5753800-5772400	Weak transcription	Brain Anterior Caudate	brain
13	chr10:5753800-5772600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:5753800-5772800	Weak transcription	Brain Hippocampus Middle	brain
15	chr10:5753800-5773200	Weak transcription	NHLF	lung
16	chr10:5753800-5783400	Weak transcription	Brain Substantia Nigra	brain
17	chr10:5753800-5787000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr10:5754000-5768600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:5754000-5772800	Weak transcription	Ovary	ovary
20	chr10:5754000-5773200	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:5754200-5773000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:5754400-5781600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr10:5754600-5765400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr10:5754600-5767600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr10:5755400-5772600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:5757000-5772800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr10:5757200-5765200	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr10:5757800-5772600	Weak transcription	Right Ventricle	heart
29	chr10:5758000-5765600	Weak transcription	Placenta	Placenta
30	chr10:5758000-5767000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr10:5758600-5772600	Weak transcription	Esophagus	oesophagus
32	chr10:5759600-5772800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr10:5759800-5765400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr10:5761000-5765600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr10:5761000-5768200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr10:5761000-5768400	Weak transcription	Fetal Lung	lung
37	chr10:5761000-5768800	Weak transcription	NHDF-Ad	bronchial
38	chr10:5761000-5772800	Weak transcription	Small Intestine	intestine
39	chr10:5761000-5773200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr10:5761400-5772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr10:5762000-5769000	Weak transcription	Hela-S3	cervix
42	chr10:5762200-5765400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr10:5762200-5766800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr10:5762200-5766800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr10:5762200-5783000	Weak transcription	Stomach Mucosa	stomach
46	chr10:5762200-5795400	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr10:5762400-5764600	Strong transcription	GM12878-XiMat	blood
48	chr10:5762400-5766000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr10:5762400-5767000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr10:5762400-5767200	Weak transcription	Pancreas	Pancrea

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