Variant report

Variant	rs17049422
Chromosome Location	chr2:58454060-58454061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:58453422..58455575-chr2:58455818..58457533,3	K562	blood:
2	chr2:58453422..58455575-chr2:58455818..58457363,2	K562	blood:
3	chr2:58448017..58451286-chr2:58451498..58454786,5	K562	blood:
4	chr2:58452149..58455977-chr2:58466804..58469435,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115392	Chromatin interaction
ENSG00000273063	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10178325	0.95[ASN][1000 genomes]
rs10490253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13417865	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13418724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13421853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17049381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17049396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17049403	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs17049406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17049408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17049420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17049431	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28588526	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28668929	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57033851	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57344611	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs57442059	0.80[AFR][1000 genomes]
rs58059919	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60176808	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140034	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62140040	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62140041	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62140043	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140045	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140046	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62140047	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140048	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62140049	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140050	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62140051	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62141871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72810371	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72810375	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72810377	0.92[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72810378	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs72810393	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72810396	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58391000-58467000	Weak transcription	HMEC	breast
2	chr2:58414000-58461400	Weak transcription	NHEK	skin
3	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:58422000-58454200	Weak transcription	Left Ventricle	heart
6	chr2:58432000-58466400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:58433600-58454200	Weak transcription	Gastric	stomach
8	chr2:58437000-58460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:58437200-58459000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:58437800-58456800	Weak transcription	Fetal Kidney	kidney
11	chr2:58438600-58454200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:58438600-58454200	Weak transcription	Aorta	Aorta
13	chr2:58438600-58454200	Weak transcription	Esophagus	oesophagus
14	chr2:58438600-58454200	Weak transcription	Fetal Brain Female	brain
15	chr2:58438600-58454200	Weak transcription	Fetal Stomach	stomach
16	chr2:58438600-58454200	Weak transcription	Lung	lung
17	chr2:58438600-58454200	Weak transcription	Pancreas	Pancrea
18	chr2:58438600-58454200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:58438600-58454200	Weak transcription	Thymus	Thymus
20	chr2:58438600-58466400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:58438800-58454200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:58438800-58454200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:58439000-58467400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:58439200-58454200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr2:58439200-58454400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:58439200-58457000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:58439200-58457600	Weak transcription	Placenta	Placenta
28	chr2:58439600-58454200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:58440000-58454200	Weak transcription	Primary B cells from cord blood	blood
30	chr2:58440000-58465000	Weak transcription	Fetal Brain Male	brain
31	chr2:58440000-58467400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:58440600-58454200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:58440600-58454400	Weak transcription	HSMM	muscle
34	chr2:58440600-58462000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:58440600-58467400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:58440800-58454200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:58440800-58454400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:58440800-58457600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:58441000-58454200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:58441000-58458200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr2:58441200-58454200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr2:58441200-58454200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr2:58443400-58454200	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr2:58443400-58454200	Weak transcription	Brain Anterior Caudate	brain
45	chr2:58443400-58454200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr2:58443400-58460400	Weak transcription	Brain Germinal Matrix	brain
47	chr2:58443600-58455600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:58443600-58462200	Weak transcription	Brain Substantia Nigra	brain
49	chr2:58444000-58454200	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:58444000-58454200	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links