Variant report

Variant	rs2089657
Chromosome Location	chr2:30470178-30470179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30470010..30473545-chr2:30474573..30477601,4	K562	blood:
2	chr2:30457464..30459532-chr2:30469414..30471477,2	MCF-7	breast:
3	chr2:30465310..30467321-chr2:30469848..30471396,2	MCF-7	breast:
4	chr2:30469843..30471764-chr2:30477374..30479207,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1001204	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10171296	0.95[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs10171305	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11676884	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13386455	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13389106	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17009304	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17009315	0.85[CEU][hapmap]
rs17321999	0.95[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1962588	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2362541	0.93[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs3813658	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3817143	0.90[EUR][1000 genomes]
rs4384829	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4564821	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4952115	0.95[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58645306	0.97[ASN][1000 genomes]
rs59693338	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6548005	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6708792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726021	0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap]
rs6732241	0.95[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72787716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787718	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72787719	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72787721	0.90[EUR][1000 genomes]
rs72787722	0.89[EUR][1000 genomes]
rs72787724	0.90[EUR][1000 genomes]
rs73925103	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7604484	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs906865	0.89[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs906866	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs906867	0.95[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9309678	0.89[EUR][1000 genomes]
rs9558	0.95[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs9798481	0.96[ASN][1000 genomes]
rs9967884	0.85[CEU][hapmap]

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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1002657	chr2:30339312-30516535	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv2662	chr2:30462905-30495134	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2089657	MPV17	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30457000-30476600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:30457200-30470400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:30457200-30473000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:30457600-30471800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:30457800-30481000	Weak transcription	Gastric	stomach
6	chr2:30458400-30475800	Weak transcription	Fetal Kidney	kidney
7	chr2:30460800-30471800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:30461000-30479800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:30461800-30472200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:30462200-30473200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:30462800-30471200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:30462800-30474800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:30462800-30475400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr2:30463000-30471000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr2:30463000-30473000	Weak transcription	Fetal Intestine Small	intestine
16	chr2:30463000-30474200	Weak transcription	Fetal Intestine Large	intestine
17	chr2:30463000-30474800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr2:30463000-30475400	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr2:30463200-30471200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:30463400-30472400	Strong transcription	HSMM	muscle
21	chr2:30463400-30473400	Weak transcription	Ovary	ovary
22	chr2:30463400-30474800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:30463400-30474800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:30463400-30475000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:30463400-30475400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:30463400-30475600	Weak transcription	Brain Germinal Matrix	brain
27	chr2:30463400-30475600	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:30463400-30475600	Weak transcription	Esophagus	oesophagus
29	chr2:30463600-30472200	Weak transcription	Lung	lung
30	chr2:30463600-30472200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:30463600-30472400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:30463600-30473200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:30463600-30475600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:30463600-30475600	Weak transcription	Osteobl	bone
35	chr2:30463800-30470400	Weak transcription	Fetal Muscle Leg	muscle
36	chr2:30463800-30472200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:30463800-30474800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:30464000-30470600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:30464200-30472400	Weak transcription	Right Atrium	heart
40	chr2:30464200-30474600	Weak transcription	Small Intestine	intestine
41	chr2:30464800-30472200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:30464800-30472200	Genic enhancers	Primary T cells from cord blood	blood
43	chr2:30465400-30474000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:30465400-30480000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:30465600-30470400	Strong transcription	Fetal Lung	lung
46	chr2:30466000-30477000	Genic enhancers	Primary B cells from peripheral blood	blood
47	chr2:30466200-30474000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr2:30466200-30476400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
49	chr2:30466200-30480400	Weak transcription	Fetal Brain Male	brain
50	chr2:30466600-30474600	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links