Variant report

Variant	rs688853
Chromosome Location	chr10:6489773-6489774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10508307	0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10508308	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10752329	0.81[EUR][1000 genomes]
rs10752330	0.87[EUR][1000 genomes]
rs10906504	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11258500	0.85[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs11258501	0.85[CEU][hapmap]
rs11258612	0.84[AMR][1000 genomes]
rs11258967	0.85[CHB][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11814744	0.93[YRI][hapmap]
rs11816284	0.84[YRI][hapmap]
rs11817284	0.92[YRI][hapmap]
rs12572911	0.85[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs12775595	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12780187	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17155850	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs17155855	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs2296125	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs34316142	0.84[AMR][1000 genomes]
rs3793724	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3793725	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3793726	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4237436	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4750422	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590467	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs593608	1.00[YRI][hapmap]
rs630196	1.00[YRI][hapmap]
rs646613	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs670804	0.93[YRI][hapmap]
rs673964	1.00[YRI][hapmap]
rs681071	0.85[CEU][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs681604	0.83[TSI][hapmap]
rs7893745	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7898408	0.84[AMR][1000 genomes]
rs7910745	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7911478	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7918923	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs961203	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][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	nsv947732	chr10:6488907-6489871	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6456200-6496600	Weak transcription	Pancreas	Pancrea
2	chr10:6464600-6490600	Strong transcription	Primary T cells from cord blood	blood
3	chr10:6465800-6496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr10:6465800-6496600	Weak transcription	Psoas Muscle	Psoas
5	chr10:6465800-6501400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:6467400-6496200	Weak transcription	Lung	lung
7	chr10:6468200-6496800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:6471200-6490200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr10:6474200-6490400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr10:6477400-6503600	Weak transcription	Gastric	stomach
11	chr10:6478800-6491000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr10:6480200-6501000	Weak transcription	Ovary	ovary
13	chr10:6480800-6497600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr10:6481200-6500200	Weak transcription	Fetal Intestine Small	intestine
15	chr10:6481400-6497800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:6484000-6496200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:6484200-6496200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr10:6484200-6496400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr10:6484600-6496600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:6487200-6490600	Genic enhancers	Fetal Thymus	thymus
21	chr10:6488200-6496200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr10:6488200-6496200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:6488200-6496200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr10:6488200-6496200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr10:6488200-6496200	Weak transcription	Brain Substantia Nigra	brain
26	chr10:6488200-6496400	Weak transcription	Adipose Nuclei	Adipose
27	chr10:6488200-6496400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr10:6488200-6497600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr10:6488200-6499600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr10:6488200-6500200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr10:6488200-6502000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr10:6488400-6490600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr10:6488400-6490800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr10:6488400-6496600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr10:6488400-6496600	Weak transcription	Brain Anterior Caudate	brain
36	chr10:6488400-6500200	Weak transcription	Esophagus	oesophagus
37	chr10:6488400-6506800	Weak transcription	K562	blood
38	chr10:6488600-6490200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr10:6488600-6490400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr10:6488600-6490400	Strong transcription	Aorta	Aorta
41	chr10:6488600-6490400	Strong transcription	Thymus	Thymus
42	chr10:6488600-6490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:6488600-6490800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr10:6488800-6490200	Strong transcription	Dnd41	blood
45	chr10:6488800-6490400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr10:6488800-6490600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:6489000-6490400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:6489200-6490600	Strong transcription	Fetal Stomach	stomach
49	chr10:6489400-6489800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
50	chr10:6489400-6490000	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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