Variant report

Variant	rs10493315
Chromosome Location	chr1:62459477-62459478
allele	G/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:31)

rs_ID	r²[population]
rs10493316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10493317	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207885	0.82[ASN][1000 genomes]
rs12562199	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12563258	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122889	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122892	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17122904	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17122915	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17122931	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1815464	0.82[ASN][1000 genomes]
rs1888988	0.83[ASN][1000 genomes]
rs2297495	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762445	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56666038	0.93[ASN][1000 genomes]
rs58529158	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59829581	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66747141	0.89[ASN][1000 genomes]
rs67035896	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67417917	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67456403	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67526244	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67622686	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67719504	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67867258	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67967624	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68081851	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72641121	0.95[ASN][1000 genomes]
rs72914071	0.93[ASN][1000 genomes]
rs72914078	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538799	1.00[ASN][1000 genomes]

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	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	esv2753481	chr1:62424207-62478878	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1005178	chr1:62439219-62468653	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv999481	chr1:62439219-62472591	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
3	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
4	chr1:62441400-62459800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:62444200-62479200	Weak transcription	Fetal Intestine Small	intestine
6	chr1:62446600-62465200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:62446600-62487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:62446800-62469400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:62447200-62469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:62447400-62481200	Weak transcription	Lung	lung
11	chr1:62448400-62470400	Weak transcription	Ovary	ovary
12	chr1:62453400-62460200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:62453600-62461400	Weak transcription	Psoas Muscle	Psoas
14	chr1:62455200-62460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:62455200-62463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:62456000-62459600	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr1:62456200-62478600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr1:62456800-62459600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:62456800-62459800	Enhancers	NHEK	skin
20	chr1:62457000-62460000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:62457000-62460000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:62457000-62460000	Strong transcription	Fetal Intestine Large	intestine
23	chr1:62457000-62473400	Weak transcription	Primary T cells from cord blood	blood
24	chr1:62457400-62459800	Weak transcription	Adipose Nuclei	Adipose
25	chr1:62457400-62460000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:62458000-62459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:62458000-62460200	Enhancers	HMEC	breast
28	chr1:62458200-62459600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:62458200-62460200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:62458400-62459600	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:62458400-62460000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:62458400-62461400	Weak transcription	Fetal Brain Female	brain
33	chr1:62458600-62459600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:62458600-62460000	Enhancers	Fetal Kidney	kidney
35	chr1:62458800-62459600	Enhancers	Placenta Amnion	Placenta Amnion
36	chr1:62458800-62460200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:62458800-62521400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr1:62459000-62459600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:62459000-62459600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:62459000-62459600	Enhancers	Stomach Mucosa	stomach
41	chr1:62459000-62484000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:62459000-62516000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:62459000-62530600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr1:62459200-62460800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:62459200-62462600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:62459200-62464800	Weak transcription	HUVEC	blood vessel
47	chr1:62459200-62487800	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:62459200-62511200	Weak transcription	Gastric	stomach
49	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr1:62459400-62459600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links