Variant report

Variant	rs6930992
Chromosome Location	chr6:27712120-27712121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27113856..27116245-chr6:27711458..27713509,2	K562	blood:
2	chr6:27705791..27707842-chr6:27711805..27713945,2	K562	blood:
3	chr6:27114745..27116366-chr6:27711280..27713509,2	K562	blood:
4	chr6:27688928..27690631-chr6:27710497..27712546,2	MCF-7	breast:
5	chr6:27694126..27696434-chr6:27711146..27712696,2	K562	blood:
6	chr6:27656133..27659088-chr6:27710854..27712483,2	K562	blood:

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000216915	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10214440	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10484401	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1139226	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13211701	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13215072	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs169262	0.83[ASN][1000 genomes]
rs1985099	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200468	0.89[ASN][1000 genomes]
rs200474	0.80[ASN][1000 genomes]
rs200475	0.82[ASN][1000 genomes]
rs200476	0.85[ASN][1000 genomes]
rs200502	0.82[CEU][hapmap]
rs2056925	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2092075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2179094	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2394000	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2394002	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2893929	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2893930	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2893931	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34752872	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35069907	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35957409	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4140646	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4711163	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4713118	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4713121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6901520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6902689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6914924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6922574	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs742046	1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs742047	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs760587	0.95[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7756968	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7760523	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7772027	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7773070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7776351	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9283880	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283881	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283882	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283883	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295740	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9295742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295743	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9295746	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9348774	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9348775	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357045	0.90[ASN][1000 genomes]
rs9366700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366702	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9368528	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368529	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9368530	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380010	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9380011	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9380012	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393847	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393848	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9461405	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9461406	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468195	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9468199	0.82[ASN][1000 genomes]
rs9468200	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468201	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468203	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468204	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468206	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468214	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9468217	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468219	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9468220	0.95[CEU][hapmap];0.87[CHB][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9468223	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468229	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6930992	AL022393.7	cis	Muscle Skeletal	GTEx
rs6930992	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs6930992	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs6930992	BTN2A2	Cis_chr	lymphoblastoid	RTeQTL
rs6930992	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs6930992	OR2B8P	cis	Thyroid	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27707000-27714600	Weak transcription	GM12878-XiMat	blood
2	chr6:27711400-27712200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:27711600-27712200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:27711600-27712200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr6:27711600-27712800	Weak transcription	K562	blood
6	chr6:27711800-27712200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:27712000-27712200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin

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