Variant report

Variant	rs11254898
Chromosome Location	chr10:5772100-5772101
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	chr10:5766311..5769267-chr10:5770852..5774721,4	K562	blood:
2	chr10:5704182..5707347-chr10:5769975..5772596,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108021	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11254115	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11254828	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11255139	0.80[ASN][1000 genomes]
rs11596959	0.87[ASW][hapmap]
rs12257412	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12571055	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12572339	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1512695	1.00[ASW][hapmap]
rs1567708	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2246268	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275772	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2669133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2669139	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797490	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797492	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2797497	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34404996	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750636	0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3793708	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793714	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3924378	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs57103262	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58502403	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59827083	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7089693	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7096328	0.92[ASN][1000 genomes]
rs73610559	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7908235	0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:5753800-5772200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr10:5753800-5772400	Weak transcription	Brain Anterior Caudate	brain
3	chr10:5753800-5772600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr10:5753800-5772800	Weak transcription	Brain Hippocampus Middle	brain
5	chr10:5753800-5773200	Weak transcription	NHLF	lung
6	chr10:5753800-5783400	Weak transcription	Brain Substantia Nigra	brain
7	chr10:5753800-5787000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr10:5754000-5772800	Weak transcription	Ovary	ovary
9	chr10:5754000-5773200	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:5754200-5773000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr10:5754400-5781600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:5755400-5772600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:5757000-5772800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr10:5757800-5772600	Weak transcription	Right Ventricle	heart
15	chr10:5758600-5772600	Weak transcription	Esophagus	oesophagus
16	chr10:5759600-5772800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:5761000-5772800	Weak transcription	Small Intestine	intestine
18	chr10:5761000-5773200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr10:5761400-5772600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr10:5762200-5783000	Weak transcription	Stomach Mucosa	stomach
21	chr10:5762200-5795400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr10:5762400-5772400	Weak transcription	HSMMtube	muscle
23	chr10:5762400-5772600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:5762400-5772600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr10:5762400-5775000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:5762400-5794600	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:5762600-5843400	Strong transcription	Dnd41	blood
28	chr10:5762800-5772600	Weak transcription	Fetal Brain Female	brain
29	chr10:5762800-5775200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr10:5762800-5778000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:5762800-5778000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:5762800-5779800	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr10:5762800-5793000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr10:5762800-5843000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:5763000-5795000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr10:5763200-5772800	Weak transcription	Aorta	Aorta
37	chr10:5763200-5778800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:5763200-5779000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:5763400-5788600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr10:5763600-5773600	Strong transcription	Fetal Thymus	thymus
41	chr10:5763800-5775000	Strong transcription	Liver	Liver
42	chr10:5764000-5772800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr10:5764200-5772600	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr10:5764200-5772600	Weak transcription	Spleen	Spleen
45	chr10:5764200-5775600	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:5764400-5773000	Weak transcription	Brain Angular Gyrus	brain
47	chr10:5764600-5773000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr10:5765400-5775800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr10:5765600-5775000	Strong transcription	Placenta	Placenta
50	chr10:5765600-5775600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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