Variant report

Variant	rs6434343
Chromosome Location	chr2:190332997-190332998
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190331421..190333100-chr2:190335308..190338236,2	K562	blood:
2	chr2:190304711..190306854-chr2:190332903..190335428,2	K562	blood:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10166420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175108	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10198663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10207812	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
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	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12613903	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12622720	0.96[ASN][1000 genomes]
rs12623394	0.93[ASN][1000 genomes]
rs12693539	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12693540	0.96[ASN][1000 genomes]
rs13009912	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13015207	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018252	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs13035381	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1356976	0.87[ASN][1000 genomes]
rs1520854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520856	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1520858	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs1520866	0.98[ASN][1000 genomes]
rs1595749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16831454	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1851104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1866605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1898971	0.96[ASN][1000 genomes]
rs1992295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2304702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2351934	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2882805	0.86[ASN][1000 genomes]
rs4309611	0.81[AMR][1000 genomes];0.97[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	0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[ASN][1000 genomes]
rs6434340	0.83[ASN][1000 genomes]
rs6434342	0.91[ASN][1000 genomes]
rs6738193	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6747222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752545	0.85[ASN][1000 genomes]
rs734859	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420765	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs744556	0.93[ASN][1000 genomes]
rs745742	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7556928	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7566093	0.85[ASN][1000 genomes]
rs7574403	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590098	0.83[AMR][1000 genomes]
rs8179541	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8179732	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs893407	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs893408	0.93[ASN][1000 genomes]
rs9677436	0.81[AFR][1000 genomes];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6434343	AC013439.4	cis	Muscle Skeletal	GTEx
rs6434343	PKIG	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190306800-190344200	Weak transcription	Esophagus	oesophagus
2	chr2:190307000-190334200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:190307600-190334200	Weak transcription	Pancreas	Pancrea
4	chr2:190307600-190338200	Weak transcription	Spleen	Spleen
5	chr2:190307600-190342000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:190307600-190342600	Weak transcription	Aorta	Aorta
7	chr2:190308000-190334600	Weak transcription	Right Ventricle	heart
8	chr2:190308200-190342800	Strong transcription	A549	lung
9	chr2:190308600-190341800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr2:190308600-190342200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:190309000-190342600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:190309200-190341200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:190309400-190337200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:190309600-190341800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:190309600-190342000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:190309800-190337000	Strong transcription	Primary B cells from cord blood	blood
17	chr2:190309800-190342400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:190310200-190340600	Strong transcription	Dnd41	blood
19	chr2:190310200-190341600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:190310400-190341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:190310800-190342000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:190310800-190342000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:190311000-190340400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:190311000-190341600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:190311000-190341800	Strong transcription	NH-A	brain
26	chr2:190311200-190341800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:190311600-190341800	Strong transcription	HMEC	breast
28	chr2:190311800-190341400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr2:190311800-190342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:190312000-190341600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:190312200-190335600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:190312200-190336400	Strong transcription	Placenta	Placenta
33	chr2:190312200-190339600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:190312200-190341200	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr2:190312200-190341400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:190312200-190341400	Strong transcription	Osteobl	bone
37	chr2:190312200-190342400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:190312600-190341200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr2:190312800-190336400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr2:190312800-190342600	Strong transcription	Fetal Thymus	thymus
41	chr2:190313000-190335600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr2:190313000-190337000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:190313000-190340400	Strong transcription	HepG2	liver
44	chr2:190313000-190342800	Strong transcription	HSMM	muscle
45	chr2:190313200-190339400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:190313200-190341600	Strong transcription	Primary B cells from peripheral blood	blood
47	chr2:190313800-190342000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr2:190315400-190334200	Weak transcription	Gastric	stomach
49	chr2:190315400-190347800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:190321200-190335000	Strong transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links