Variant report

Variant	rs6710755
Chromosome Location	chr2:73343973-73343974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73338429..73340755-chr2:73343123..73345706,2	K562	blood:
2	chr2:73338342..73340040-chr2:73341941..73344372,2	MCF-7	breast:
3	chr2:73317548..73319576-chr2:73341568..73344564,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135631	Chromatin interaction
ENSG00000272702	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10166220	0.86[JPT][hapmap]
rs10167566	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10174548	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10176939	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs10180720	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs10180995	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.94[ASN][1000 genomes]
rs10189744	0.86[JPT][hapmap]
rs10190861	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10192077	0.83[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.88[YRI][hapmap]
rs10197305	0.81[JPT][hapmap]
rs10203608	0.90[ASN][1000 genomes]
rs1046186	0.91[ASN][1000 genomes]
rs10865396	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11126389	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11686557	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11885522	0.96[ASN][1000 genomes]
rs12104691	0.94[ASN][1000 genomes]
rs12614059	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13018842	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13019020	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13385994	0.91[ASN][1000 genomes]
rs13388404	0.86[JPT][hapmap]
rs13391532	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13393567	0.89[ASN][1000 genomes]
rs13400920	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs13400948	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs13403757	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs13403781	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs13407719	0.89[ASN][1000 genomes]
rs13416407	0.95[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13427947	0.91[ASN][1000 genomes]
rs1370383	0.80[JPT][hapmap];0.86[MEX][hapmap]
rs1430349	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.99[ASN][1000 genomes]
rs1430350	0.96[ASN][1000 genomes]
rs1430351	0.96[ASN][1000 genomes]
rs17008571	0.81[JPT][hapmap]
rs17008631	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs1864488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992133	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2421098	0.84[CHD][hapmap];0.86[JPT][hapmap]
rs35131031	0.88[ASN][1000 genomes]
rs3813222	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3813223	0.91[ASN][1000 genomes]
rs3901273	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4144837	0.86[JPT][hapmap]
rs4514897	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs4591365	0.96[ASN][1000 genomes]
rs55894650	0.92[ASN][1000 genomes]
rs57536428	0.88[ASN][1000 genomes]
rs57701326	0.96[ASN][1000 genomes]
rs57726945	0.99[ASN][1000 genomes]
rs57937746	0.88[ASN][1000 genomes]
rs6546796	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs6546797	0.87[LWK][hapmap];0.86[MEX][hapmap];0.88[YRI][hapmap]
rs6546800	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6546801	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6709938	0.81[JPT][hapmap]
rs6710739	0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs6711891	0.81[JPT][hapmap];0.86[MEX][hapmap]
rs6712925	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6719333	0.86[JPT][hapmap];0.85[YRI][hapmap]
rs6720817	0.90[ASN][1000 genomes]
rs6727919	0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs6729266	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6732369	0.80[CHD][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap]
rs6736153	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6749237	0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6750069	0.81[JPT][hapmap];0.85[YRI][hapmap]
rs6757131	0.81[JPT][hapmap]
rs727470	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs727471	0.94[ASN][1000 genomes]
rs732180	0.85[JPT][hapmap]
rs7557173	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7559074	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7559340	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7566904	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs7567413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7570459	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7570876	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs7579770	0.81[JPT][hapmap]
rs7593322	0.96[ASN][1000 genomes]
rs7596830	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597032	0.81[JPT][hapmap]
rs7599657	0.96[ASN][1000 genomes]
rs7602651	1.00[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.81[YRI][hapmap];0.99[ASN][1000 genomes]
rs891432	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs891433	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs893258	0.81[JPT][hapmap]
rs893259	0.81[JPT][hapmap]
rs9309471	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1006801	chr2:73305056-73431711	Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6710755	SFXN5	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73340800-73344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:73341200-73344200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr2:73341400-73344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:73341600-73344200	Weak transcription	Hela-S3	cervix
5	chr2:73341600-73344400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr2:73342200-73344000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:73342200-73344200	Weak transcription	NHDF-Ad	bronchial
8	chr2:73342200-73344200	Weak transcription	NHLF	lung
9	chr2:73342200-73344400	Weak transcription	Osteobl	bone
10	chr2:73342400-73344200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:73342400-73344200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:73343600-73345600	Enhancers	Placenta	Placenta

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