Variant report

Variant	rs539103
Chromosome Location	chr10:6504253-6504254
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11258964	0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs11258984	1.00[CHB][hapmap];0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs4750429	0.82[EUR][1000 genomes]
rs4750432	0.82[EUR][1000 genomes]
rs542817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs545417	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs593608	1.00[EUR][1000 genomes]
rs601512	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs602419	0.90[EUR][1000 genomes]
rs615256	1.00[EUR][1000 genomes]
rs616080	1.00[EUR][1000 genomes]
rs618020	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs619761	0.90[EUR][1000 genomes]
rs629244	1.00[EUR][1000 genomes]
rs630196	1.00[EUR][1000 genomes]
rs636819	0.82[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs637297	0.82[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648072	0.90[EUR][1000 genomes]
rs651486	1.00[EUR][1000 genomes]
rs658344	1.00[EUR][1000 genomes]
rs6602704	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs663532	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6488400-6506800	Weak transcription	K562	blood
2	chr10:6493400-6516200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr10:6496000-6508200	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr10:6496200-6506200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:6496200-6508200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr10:6496200-6509000	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr10:6496200-6511600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
8	chr10:6496200-6513000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:6496200-6514000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr10:6496200-6514200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:6496200-6514600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr10:6496600-6506400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:6497600-6513200	Strong transcription	Primary T cells from cord blood	blood
15	chr10:6498400-6537000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr10:6498600-6506000	Strong transcription	Primary hematopoietic stem cells	blood
17	chr10:6498600-6508800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr10:6498600-6510000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr10:6498600-6512000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr10:6498600-6518800	Weak transcription	Fetal Stomach	stomach
21	chr10:6499000-6507600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr10:6499000-6527800	Weak transcription	Pancreas	Pancrea
23	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
24	chr10:6500200-6504400	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:6500200-6510200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr10:6501000-6513800	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:6501200-6506400	Weak transcription	Brain Substantia Nigra	brain
28	chr10:6501400-6506200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr10:6501400-6510000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:6501600-6527200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr10:6501800-6505200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:6501800-6508200	Weak transcription	Fetal Intestine Small	intestine
33	chr10:6501800-6509200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr10:6501800-6509400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr10:6501800-6511000	Weak transcription	Aorta	Aorta
36	chr10:6501800-6513800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr10:6501800-6513800	Strong transcription	Fetal Thymus	thymus
38	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:6502000-6505400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr10:6502000-6511200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr10:6502200-6518800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr10:6502600-6506200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:6502800-6506200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr10:6503000-6513000	Weak transcription	Psoas Muscle	Psoas
45	chr10:6503000-6533000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr10:6503200-6510200	Strong transcription	Thymus	Thymus
47	chr10:6503200-6513600	Strong transcription	Dnd41	blood
48	chr10:6503200-6513800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr10:6503200-6516000	Weak transcription	Brain Angular Gyrus	brain
50	chr10:6503600-6506200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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