Variant report

Variant	rs2647257
Chromosome Location	chr4:106199505-106199506
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	chr4:106197623..106199957-chr4:106222929..106225459,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1032625	0.99[ASN][1000 genomes]
rs10461139	0.89[ASN][1000 genomes]
rs11097882	0.83[ASN][1000 genomes]
rs11721948	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11726786	0.81[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11735256	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12639764	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12645144	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13103161	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13109676	0.91[ASN][1000 genomes]
rs13147502	0.88[ASN][1000 genomes]
rs1391439	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1541374	0.91[YRI][hapmap]
rs2007403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2047409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2088483	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2454205	0.95[ASN][1000 genomes]
rs2454206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647244	0.98[ASN][1000 genomes]
rs2647250	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs2647251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647268	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2726459	0.98[ASN][1000 genomes]
rs2726460	0.91[ASN][1000 genomes]
rs2726491	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2726519	0.93[ASN][1000 genomes]
rs2726520	0.93[ASN][1000 genomes]
rs2726521	0.95[ASN][1000 genomes]
rs34104813	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699165	0.95[ASN][1000 genomes]
rs55838312	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62330911	0.91[ASN][1000 genomes]
rs62331159	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62332760	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6818637	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6855629	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[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7658539	0.92[ASN][1000 genomes]
rs7661349	0.92[ASW][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.91[YRI][hapmap]
rs7670522	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7683416	0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2647257	PPA2	cis	Lymphoblastoid	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106178000-106201000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr4:106179200-106201000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr4:106187200-106202000	Weak transcription	Stomach Mucosa	stomach
4	chr4:106188800-106199800	Strong transcription	GM12878-XiMat	blood
5	chr4:106196600-106202000	Weak transcription	Psoas Muscle	Psoas
6	chr4:106197200-106200000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:106197400-106201600	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:106197400-106201800	Weak transcription	NHEK	skin
9	chr4:106197400-106202000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:106197400-106210200	Weak transcription	Small Intestine	intestine
11	chr4:106197600-106201400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr4:106197600-106202000	Weak transcription	Aorta	Aorta
13	chr4:106197600-106204000	Weak transcription	Fetal Intestine Small	intestine
14	chr4:106197800-106199600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:106197800-106199600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:106197800-106199600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:106197800-106199600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:106197800-106199600	Weak transcription	Gastric	stomach
19	chr4:106197800-106200200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:106197800-106200200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr4:106197800-106200800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr4:106197800-106201000	Weak transcription	NHDF-Ad	bronchial
23	chr4:106197800-106201200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:106197800-106201200	Weak transcription	HSMMtube	muscle
25	chr4:106197800-106201400	Weak transcription	Fetal Lung	lung
26	chr4:106197800-106201400	Weak transcription	HUVEC	blood vessel
27	chr4:106197800-106202000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:106197800-106202000	Weak transcription	Adipose Nuclei	Adipose
29	chr4:106197800-106202000	Weak transcription	Brain Anterior Caudate	brain
30	chr4:106197800-106202000	Weak transcription	Pancreas	Pancrea
31	chr4:106197800-106202000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr4:106197800-106202200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr4:106197800-106202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr4:106197800-106203200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr4:106197800-106204000	Weak transcription	Primary T cells from cord blood	blood
36	chr4:106197800-106204000	Weak transcription	Fetal Kidney	kidney
37	chr4:106198000-106199600	Weak transcription	Thymus	Thymus
38	chr4:106198000-106199800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:106198000-106199800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:106198000-106199800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:106198000-106199800	Weak transcription	Spleen	Spleen
42	chr4:106198000-106201000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:106198000-106201200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:106198000-106201200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:106198000-106201200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:106198000-106201200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:106198000-106201200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:106198000-106201200	Weak transcription	NH-A	brain
49	chr4:106198000-106201200	Weak transcription	Osteobl	bone
50	chr4:106198000-106201400	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links