Variant report

Variant	rs13428557
Chromosome Location	chr2:86015289-86015290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86007740..86010052-chr2:86013062..86015438,2	K562	blood:
2	chr2:86015229..86018634-chr2:86021632..86024903,4	K562	blood:
3	chr2:85980611..85983485-chr2:86014274..86016062,2	MCF-7	breast:
4	chr2:86013750..86016057-chr2:86037086..86038756,2	K562	blood:
5	chr2:86013683..86016312-chr2:86025949..86028304,2	MCF-7	breast:
6	chr2:86012601..86015321-chr2:86017209..86019068,2	K562	blood:
7	chr2:86005993..86008298-chr2:86013315..86016426,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168874	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10190632	0.85[CHB][hapmap]
rs10207516	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13386681	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13392366	0.82[EUR][1000 genomes]
rs13402783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370545	0.83[CEU][hapmap]
rs2001593	0.82[EUR][1000 genomes]
rs2139198	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs35976024	0.82[ASN][1000 genomes]
rs3731826	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55882144	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs727123	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs869778	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86001400-86023000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:86001600-86020000	Weak transcription	Fetal Brain Female	brain
3	chr2:86001600-86023000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:86002200-86015800	Weak transcription	A549	lung
5	chr2:86004800-86017200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:86005400-86019200	Weak transcription	HUVEC	blood vessel
7	chr2:86006600-86019000	Weak transcription	Esophagus	oesophagus
8	chr2:86006800-86020000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:86007000-86015400	Weak transcription	Brain Angular Gyrus	brain
10	chr2:86007000-86019200	Weak transcription	Hela-S3	cervix
11	chr2:86008200-86016000	Weak transcription	Pancreas	Pancrea
12	chr2:86012000-86016400	Enhancers	Right Atrium	heart
13	chr2:86012000-86019000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:86012200-86015600	Weak transcription	Brain Substantia Nigra	brain
15	chr2:86012200-86015600	Bivalent Enhancer	Fetal Stomach	stomach
16	chr2:86012400-86016400	Genic enhancers	Right Ventricle	heart
17	chr2:86012800-86015600	Enhancers	HepG2	liver
18	chr2:86013200-86015400	Genic enhancers	Spleen	Spleen
19	chr2:86013200-86015800	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr2:86013200-86016000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:86013200-86017200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:86013200-86017400	Weak transcription	Brain Germinal Matrix	brain
23	chr2:86013200-86023000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:86013400-86017400	Weak transcription	NH-A	brain
25	chr2:86013400-86019000	Weak transcription	Psoas Muscle	Psoas
26	chr2:86013600-86015400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr2:86013600-86015800	Genic enhancers	Aorta	Aorta
28	chr2:86013600-86017400	Strong transcription	Adipose Nuclei	Adipose
29	chr2:86013600-86017800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:86013600-86019000	Weak transcription	NHDF-Ad	bronchial
31	chr2:86013600-86023200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr2:86013800-86015400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:86013800-86016800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:86013800-86019200	Weak transcription	HSMMtube	muscle
35	chr2:86014000-86015800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:86014000-86015800	Genic enhancers	Stomach Smooth Muscle	stomach
37	chr2:86014000-86015800	Strong transcription	NHLF	lung
38	chr2:86014000-86015800	Strong transcription	Osteobl	bone
39	chr2:86014000-86016000	Strong transcription	Brain Anterior Caudate	brain
40	chr2:86014000-86016000	Strong transcription	Fetal Muscle Leg	muscle
41	chr2:86014000-86016000	Strong transcription	Gastric	stomach
42	chr2:86014000-86016200	Strong transcription	Fetal Intestine Small	intestine
43	chr2:86014000-86017000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:86014000-86017800	Strong transcription	Fetal Lung	lung
45	chr2:86014000-86019000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:86014000-86019600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:86014200-86015600	Weak transcription	Fetal Heart	heart
48	chr2:86014200-86015600	Strong transcription	Ovary	ovary
49	chr2:86014200-86017400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr2:86014200-86023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links