Variant report

Variant	rs11259245
Chromosome Location	chr10:6541923-6541924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10906712	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11259211	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11259372	0.86[AFR][1000 genomes]
rs11259531	1.00[AFR][1000 genomes]
rs11597105	1.00[MKK][hapmap]
rs41367851	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.92[ASN][1000 genomes]
rs4748099	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7918373	1.00[MKK][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv5687	chr10:6537209-6556751	Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
2	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:6518200-6556800	Weak transcription	Fetal Intestine Large	intestine
6	chr10:6519200-6544400	Weak transcription	Spleen	Spleen
7	chr10:6526600-6553000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:6527400-6542000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:6529000-6546200	Weak transcription	Esophagus	oesophagus
10	chr10:6529000-6552800	Weak transcription	Lung	lung
11	chr10:6530400-6552600	Weak transcription	K562	blood
12	chr10:6533800-6552800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:6534400-6545800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr10:6535400-6553400	Weak transcription	Gastric	stomach
15	chr10:6536600-6552800	Weak transcription	Fetal Intestine Small	intestine
16	chr10:6537400-6552800	Weak transcription	Fetal Stomach	stomach
17	chr10:6537600-6544200	Weak transcription	Pancreas	Pancrea
18	chr10:6537600-6552600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr10:6537800-6543800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr10:6537800-6548600	Weak transcription	Brain Hippocampus Middle	brain
21	chr10:6537800-6548800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr10:6538000-6546800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr10:6538200-6552800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr10:6539200-6542000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:6539600-6542000	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr10:6539600-6542000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr10:6539600-6542200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr10:6539800-6542000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr10:6539800-6542000	Genic enhancers	Dnd41	blood
30	chr10:6540000-6542000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr10:6540000-6542000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr10:6540200-6542000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:6540200-6542000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr10:6540200-6542000	Genic enhancers	Fetal Thymus	thymus
35	chr10:6540200-6548800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:6540800-6542800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr10:6540800-6552200	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr10:6540800-6552800	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr10:6540800-6556600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr10:6541000-6542600	Weak transcription	Brain Angular Gyrus	brain
41	chr10:6541000-6544000	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr10:6541200-6542000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr10:6541200-6542200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr10:6541200-6543000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
45	chr10:6541200-6544200	Weak transcription	Psoas Muscle	Psoas
46	chr10:6541200-6546600	Strong transcription	Thymus	Thymus
47	chr10:6541400-6542000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr10:6541400-6542000	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr10:6541400-6542000	Weak transcription	HMEC	breast
50	chr10:6541400-6542800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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