Variant report

Variant	rs2073134
Chromosome Location	chr6:39464712-39464713
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:39463170..39464911-chr6:39479174..39481419,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11751784	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11962587	0.80[CHB][hapmap]
rs11968704	0.80[CHB][hapmap]
rs11969059	0.85[CHB][hapmap]
rs1328387	0.89[ASW][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs1410487	0.90[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1546910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16892158	0.80[CHB][hapmap]
rs17457401	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927774	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs1927775	0.85[CHB][hapmap]
rs1952362	0.84[CHB][hapmap];0.86[CHD][hapmap]
rs2026670	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2235817	0.80[CHB][hapmap]
rs2273063	0.80[CHB][hapmap]
rs4236064	0.80[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs4254985	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4446568	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482968	0.80[CHB][hapmap]
rs4540261	0.90[CHB][hapmap];0.81[CHD][hapmap]
rs4714255	0.80[CHB][hapmap]
rs4714256	0.85[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs55860200	0.84[ASN][1000 genomes]
rs56951565	0.85[ASN][1000 genomes]
rs58087685	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6458117	0.89[ASW][hapmap];0.80[MEX][hapmap]
rs6901155	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs6919556	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922624	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6930913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6942355	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9296298	0.90[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap]
rs9296299	0.80[CHB][hapmap]
rs9296300	0.90[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs9357306	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9357307	0.84[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs9357309	0.80[CHB][hapmap]
rs9357310	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9367008	0.85[CHB][hapmap]
rs9367009	0.85[CHB][hapmap]
rs9367014	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9367015	0.91[ASN][1000 genomes]
rs9367017	0.86[ASN][1000 genomes]
rs9369119	0.90[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap]
rs9369122	0.81[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9380863	0.85[CHB][hapmap]
rs9380868	0.83[CHB][hapmap]
rs9380874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380875	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9394599	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs9394600	0.80[CHB][hapmap]
rs9394602	0.80[CHB][hapmap]
rs9394606	0.80[CHB][hapmap]
rs9394610	0.90[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9462553	0.85[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs9471113	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs9471118	0.90[ASN][1000 genomes]
rs9471128	0.89[ASW][hapmap];0.80[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885822	chr6:39327708-39721216	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv885823	chr6:39421715-39526867	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2073134	CRIP3	cis	cerebellum	SCAN
rs2073134	CCND3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39455400-39465200	Weak transcription	Right Atrium	heart
2	chr6:39456800-39468400	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:39461600-39464800	Weak transcription	NHDF-Ad	bronchial
4	chr6:39461800-39464800	Weak transcription	Placenta	Placenta
5	chr6:39461800-39465200	Weak transcription	Fetal Kidney	kidney
6	chr6:39462000-39465000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:39462600-39466200	Enhancers	Fetal Lung	lung
8	chr6:39462800-39465000	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:39462800-39465000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr6:39462800-39467000	Enhancers	Fetal Stomach	stomach
11	chr6:39463000-39466400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr6:39463800-39464800	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:39463800-39465000	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:39463800-39465600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:39464000-39465600	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr6:39464200-39465200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:39464200-39465400	Enhancers	Adipose Nuclei	Adipose
18	chr6:39464200-39466000	Enhancers	Ovary	ovary
19	chr6:39464400-39464800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:39464400-39466400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:39464600-39465400	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr6:39464600-39465600	Enhancers	Rectal Smooth Muscle	rectum

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