Variant report

Variant	rs734859
Chromosome Location	chr2:190342069-190342070
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190338740..190340819-chr2:190341888..190343639,2	K562	blood:
2	chr2:190341307..190343721-chr2:190345345..190347093,2	MCF-7	breast:
3	chr2:190341305..190342866-chr2:190363155..190365858,2	K562	blood:
4	chr2:190341340..190343913-chr2:190441363..190443168,2	K562	blood:
5	chr2:190339500..190342823-chr2:190342952..190345500,4	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10166420	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175108	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10198663	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10210634	0.85[ASN][1000 genomes]
rs10804029	0.81[ASN][1000 genomes]
rs10931417	0.85[ASN][1000 genomes]
rs11677167	0.85[ASN][1000 genomes]
rs11678414	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613903	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12622720	0.96[ASN][1000 genomes]
rs12623394	0.93[ASN][1000 genomes]
rs12693539	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693540	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13009912	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13015207	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018252	0.87[ASN][1000 genomes]
rs13035381	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356976	0.87[ASN][1000 genomes]
rs1520854	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520856	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520866	0.98[ASN][1000 genomes]
rs1595749	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831454	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1851104	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1866605	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1898971	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1992295	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304702	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2351934	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2882805	0.86[ASN][1000 genomes]
rs4309611	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4580411	0.83[ASN][1000 genomes]
rs4666775	0.98[ASN][1000 genomes]
rs4667280	0.84[ASN][1000 genomes]
rs4667284	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6434340	0.83[ASN][1000 genomes]
rs6434342	0.91[ASN][1000 genomes]
rs6434343	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738193	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747222	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752545	0.85[ASN][1000 genomes]
rs744556	0.93[ASN][1000 genomes]
rs745742	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7556928	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7566093	0.85[ASN][1000 genomes]
rs7574403	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8179541	1.00[ASN][1000 genomes]
rs8179732	1.00[ASN][1000 genomes]
rs893407	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs893408	0.93[ASN][1000 genomes]
rs9677436	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875615	chr2:190215527-190444392	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv584062	chr2:190272195-190376493	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs734859	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190306800-190344200	Weak transcription	Esophagus	oesophagus
2	chr2:190307600-190342600	Weak transcription	Aorta	Aorta
3	chr2:190308200-190342800	Strong transcription	A549	lung
4	chr2:190308600-190342200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:190309000-190342600	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:190309800-190342400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:190311800-190342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr2:190312200-190342400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:190312800-190342600	Strong transcription	Fetal Thymus	thymus
10	chr2:190313000-190342800	Strong transcription	HSMM	muscle
11	chr2:190315400-190347800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:190325600-190342600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:190330600-190342200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:190330600-190342600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:190331600-190342600	Strong transcription	GM12878-XiMat	blood
16	chr2:190332400-190342400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:190333000-190347200	Weak transcription	Small Intestine	intestine
18	chr2:190333400-190344200	Weak transcription	Stomach Mucosa	stomach
19	chr2:190334800-190342600	Weak transcription	Brain Substantia Nigra	brain
20	chr2:190335000-190342800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:190335000-190343200	Weak transcription	Colonic Mucosa	Colon
22	chr2:190335000-190348600	Weak transcription	Pancreas	Pancrea
23	chr2:190335000-190348600	Weak transcription	Right Ventricle	heart
24	chr2:190335000-190348800	Weak transcription	Gastric	stomach
25	chr2:190335000-190351800	Weak transcription	Psoas Muscle	Psoas
26	chr2:190335000-190366200	Weak transcription	Ovary	ovary
27	chr2:190335800-190342600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:190335800-190352600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:190336600-190349600	Weak transcription	HSMMtube	muscle
30	chr2:190337000-190342400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:190337400-190342200	Weak transcription	Hela-S3	cervix
32	chr2:190338400-190348600	Weak transcription	Fetal Intestine Small	intestine
33	chr2:190338600-190346000	Weak transcription	Thymus	Thymus
34	chr2:190338600-190348600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:190338600-190349600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:190339400-190342400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:190339400-190343200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:190339400-190344200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:190339400-190349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr2:190339600-190342600	Weak transcription	Brain Anterior Caudate	brain
41	chr2:190339600-190342600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr2:190339600-190342800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:190339600-190343000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr2:190339600-190344200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:190339600-190344400	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:190339600-190348200	Weak transcription	Lung	lung
47	chr2:190339600-190348400	Weak transcription	Spleen	Spleen
48	chr2:190339600-190349800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:190339600-190350000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr2:190339600-190352600	Weak transcription	Colon Smooth Muscle	Colon

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