Variant report

Variant	rs1409397
Chromosome Location	chr10:22900143-22900144
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:22898960..22901520-chr10:22921454..22923581,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10764341	0.81[CEU][hapmap]
rs11013054	1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1171496	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs1171505	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs1409398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1750750	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1750754	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1750755	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1750756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1750757	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1750758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778303	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778304	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1778316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778351	0.88[JPT][hapmap]
rs1778353	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1778355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778356	0.89[JPT][hapmap]
rs2256542	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2364116	0.85[ASN][1000 genomes]
rs2559522	0.89[JPT][hapmap]
rs2559523	0.89[JPT][hapmap]
rs2559524	0.88[JPT][hapmap]
rs2559526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2559527	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2559528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2765994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765995	0.89[JPT][hapmap]
rs2765997	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs2765998	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798982	0.89[JPT][hapmap]
rs2913109	0.89[JPT][hapmap]
rs2913110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7071450	1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs7098460	0.89[JPT][hapmap]
rs7099314	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs754822	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7912144	0.89[JPT][hapmap]
rs943194	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs943195	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830947	chr10:22881196-23004381	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22844200-22904800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr10:22858200-22904000	Weak transcription	Colonic Mucosa	Colon
3	chr10:22862400-22902000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:22880000-22906800	Weak transcription	Colon Smooth Muscle	Colon
5	chr10:22887200-22902400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:22888800-22905000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr10:22889400-22904400	Weak transcription	Hela-S3	cervix
8	chr10:22891000-22901400	Weak transcription	Gastric	stomach
9	chr10:22891000-22904800	Weak transcription	Right Ventricle	heart
10	chr10:22891200-22904800	Weak transcription	NHLF	lung
11	chr10:22893600-22902000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:22894000-22902600	Weak transcription	Right Atrium	heart
13	chr10:22894000-22906600	Weak transcription	Ovary	ovary
14	chr10:22894200-22904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr10:22894600-22903000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr10:22894600-22904400	Weak transcription	NHDF-Ad	bronchial
17	chr10:22894600-22904600	Weak transcription	NHEK	skin
18	chr10:22894600-22905000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:22894800-22904600	Weak transcription	Adipose Nuclei	Adipose
20	chr10:22894800-22913000	Weak transcription	Fetal Kidney	kidney
21	chr10:22895400-22904600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:22895600-22901000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr10:22895600-22902000	Weak transcription	Pancreas	Pancrea
24	chr10:22895600-22902200	Weak transcription	Placenta	Placenta
25	chr10:22895600-22906000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:22895800-22900200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:22895800-22904600	Weak transcription	HUVEC	blood vessel
28	chr10:22895800-22904800	Weak transcription	NH-A	brain
29	chr10:22896000-22902600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:22896200-22901600	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr10:22896400-22904000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:22896400-22904600	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr10:22896400-22904600	Weak transcription	A549	lung
34	chr10:22896400-22904800	Weak transcription	Osteobl	bone
35	chr10:22896600-22902200	Weak transcription	Esophagus	oesophagus
36	chr10:22896600-22904600	Weak transcription	HSMM	muscle
37	chr10:22897200-22900400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr10:22897200-22901000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr10:22897200-22907000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr10:22897400-22901200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr10:22897400-22901200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr10:22897400-22901400	Weak transcription	Lung	lung
43	chr10:22897400-22901800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr10:22897400-22904800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr10:22897600-22904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr10:22897800-22901000	Weak transcription	Aorta	Aorta
47	chr10:22897800-22901000	Weak transcription	Fetal Intestine Small	intestine
48	chr10:22897800-22901400	Weak transcription	Fetal Stomach	stomach
49	chr10:22897800-22904000	Weak transcription	Left Ventricle	heart
50	chr10:22897800-22904600	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links