Variant report

Variant	rs10493316
Chromosome Location	chr1:62458463-62458464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10493315	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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[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]
rs12084877	0.82[JPT][hapmap]
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]
rs12728194	0.82[CHB][hapmap]
rs17122889	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122892	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[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[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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:51 , 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	chr1:62447000-62459000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:62447200-62469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:62447400-62481200	Weak transcription	Lung	lung
12	chr1:62448200-62458600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:62448400-62470400	Weak transcription	Ovary	ovary
14	chr1:62448600-62459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:62453400-62460200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:62453600-62461400	Weak transcription	Psoas Muscle	Psoas
17	chr1:62455200-62460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:62455200-62463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:62456000-62459000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:62456000-62459600	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr1:62456200-62478600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr1:62456600-62459200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:62456800-62459000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:62456800-62459000	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr1:62456800-62459600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:62456800-62459800	Enhancers	NHEK	skin
27	chr1:62457000-62458800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:62457000-62459000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr1:62457000-62459400	Strong transcription	Liver	Liver
30	chr1:62457000-62460000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:62457000-62460000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:62457000-62460000	Strong transcription	Fetal Intestine Large	intestine
33	chr1:62457000-62473400	Weak transcription	Primary T cells from cord blood	blood
34	chr1:62457200-62459200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr1:62457400-62458600	Weak transcription	Fetal Kidney	kidney
36	chr1:62457400-62458600	Weak transcription	Left Ventricle	heart
37	chr1:62457400-62458800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:62457400-62459800	Weak transcription	Adipose Nuclei	Adipose
39	chr1:62457400-62460000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:62458000-62459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:62458000-62460200	Enhancers	HMEC	breast
42	chr1:62458200-62459000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:62458200-62459200	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:62458200-62459400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:62458200-62459600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:62458200-62460200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:62458400-62458800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:62458400-62459200	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:62458400-62459600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:62458400-62460000	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links