Variant report

Variant	rs2973445
Chromosome Location	chr5:90415585-90415586
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90413771..90418676-chr5:90419460..90425678,7	K562	blood:
2	chr5:90414268..90417626-chr5:90676737..90680178,4	K562	blood:
3	chr5:90399443..90402350-chr5:90413379..90415651,2	MCF-7	breast:
4	chr5:90414268..90419029-chr5:90677575..90681410,6	K562	blood:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12109264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16869403	0.81[CEU][hapmap]
rs16869404	0.90[CEU][hapmap]
rs16869414	0.90[CEU][hapmap]
rs16869425	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1852731	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1876635	0.81[CEU][hapmap]
rs1986718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886924	0.80[CEU][hapmap]
rs2950849	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2950850	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950852	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950853	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2950855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973444	0.90[CEU][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2973447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973449	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973454	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973455	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2973456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112484	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3952745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56377639	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58524182	0.82[AMR][1000 genomes]
rs59654682	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66482530	0.80[EUR][1000 genomes]
rs6874106	0.90[CEU][hapmap]
rs73189007	1.00[ASN][1000 genomes]
rs73189008	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90396200-90422800	Weak transcription	Esophagus	oesophagus
2	chr5:90401600-90431800	Weak transcription	K562	blood
3	chr5:90403000-90415600	Weak transcription	Right Atrium	heart
4	chr5:90403000-90431600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:90403200-90431600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90403400-90418800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:90403400-90418800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:90406600-90421800	Weak transcription	Small Intestine	intestine
9	chr5:90406800-90418600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr5:90407200-90415800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr5:90407600-90416000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:90409200-90418400	Weak transcription	Fetal Brain Female	brain
13	chr5:90410800-90415600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:90410800-90419200	Weak transcription	Brain Anterior Caudate	brain
15	chr5:90411000-90415600	Weak transcription	Adipose Nuclei	Adipose
16	chr5:90411000-90416200	Weak transcription	Fetal Stomach	stomach
17	chr5:90411000-90421600	Weak transcription	Brain Hippocampus Middle	brain
18	chr5:90413800-90415800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:90413800-90416200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr5:90414000-90416800	Enhancers	Fetal Lung	lung
21	chr5:90414000-90420000	Enhancers	NHDF-Ad	bronchial
22	chr5:90414200-90416600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:90414200-90417400	Enhancers	Colon Smooth Muscle	Colon
24	chr5:90414400-90416200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr5:90414400-90416600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:90414400-90416600	Enhancers	Fetal Intestine Small	intestine
27	chr5:90414600-90416000	Enhancers	Rectal Smooth Muscle	rectum
28	chr5:90414600-90416600	Enhancers	Fetal Heart	heart
29	chr5:90414600-90418400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:90414600-90419000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:90414800-90416200	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr5:90414800-90418600	Weak transcription	NHLF	lung
33	chr5:90414800-90420600	Enhancers	Stomach Smooth Muscle	stomach
34	chr5:90415000-90416000	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr5:90415000-90416000	Enhancers	Pancreas	Pancrea
36	chr5:90415000-90416200	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr5:90415000-90416600	Enhancers	Fetal Muscle Leg	muscle
38	chr5:90415000-90421800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:90415200-90415600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:90415200-90415800	Weak transcription	Aorta	Aorta
41	chr5:90415200-90416000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr5:90415200-90416000	Enhancers	Left Ventricle	heart
43	chr5:90415200-90416000	Enhancers	Ovary	ovary
44	chr5:90415200-90416400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr5:90415200-90416600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:90415400-90416600	Enhancers	Fetal Intestine Large	intestine
47	chr5:90415400-90418600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr5:90415400-90418800	Weak transcription	Psoas Muscle	Psoas
49	chr5:90415400-90419600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr5:90415400-90419600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links