Variant report

Variant	rs7747454
Chromosome Location	chr6:27034253-27034254
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27020688..27023464-chr6:27032968..27035001,2	K562	blood:
2	chr6:26922078..26923970-chr6:27032946..27034480,2	K562	blood:
3	chr6:26986842..26988770-chr6:27031968..27034490,2	K562	blood:

Variant related genes	Relation type
ENSG00000224843	Chromatin interaction
ENSG00000238621	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1028308	0.84[JPT][hapmap]
rs10456351	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10456352	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946891	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10946892	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946893	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10946897	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946898	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11754305	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11756275	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12189814	0.85[ASW][hapmap];0.91[YRI][hapmap]
rs12193875	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12201034	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12201393	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12209886	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12211984	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12523820	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12527111	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527231	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12661756	0.85[TSI][hapmap]
rs13212021	0.97[ASN][1000 genomes]
rs13217675	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2022272	0.90[JPT][hapmap];0.87[MEX][hapmap];0.81[MKK][hapmap]
rs2057348	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2142685	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2393915	0.85[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs35691005	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3999229	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4269366	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4358615	0.85[TSI][hapmap]
rs4403259	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4422620	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4424065	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4434464	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4476823	0.82[ASN][1000 genomes]
rs4509113	0.92[ASN][1000 genomes]
rs4583981	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4713066	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4713069	0.90[JPT][hapmap]
rs62401067	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62402054	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6456766	0.81[ASN][1000 genomes]
rs6456767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6456768	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6921388	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs6930508	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6937880	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.98[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7451149	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7739845	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7744759	0.90[JPT][hapmap]
rs7764984	0.81[ASN][1000 genomes]
rs7768407	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs858964	0.85[JPT][hapmap]
rs9295730	0.85[JPT][hapmap]
rs9379955	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379956	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379958	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379960	0.85[JPT][hapmap]
rs9393789	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393790	0.90[JPT][hapmap]
rs9393791	0.85[JPT][hapmap]
rs9461330	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9467936	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9467978	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs994691	0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	esv2758038	chr6:26695219-27095714	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
3	esv2759410	chr6:26695219-27095714	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv1029124	chr6:26825468-27109774	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	244 gene(s)	inside rSNPs	diseases
5	nsv471636	chr6:26841084-27038175	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv469625	chr6:26893739-27038175	Flanking Active TSS Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv482537	chr6:26893739-27038175	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv965631	chr6:27007405-27037069	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3369822	chr6:27007480-27037513	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7747454	HIST1H2BH	cis	cerebellum	SCAN
rs7747454	RP11-457M11.5	cis	Stomach	GTEx
rs7747454	RP11-457M11.5	cis	Whole Blood	GTEx
rs7747454	HMGN4	cis	lymphoblastoid	seeQTL
rs7747454	RP11-457M11.5	cis	Thyroid	GTEx
rs7747454	PRSS16	cis	cerebellum	SCAN
rs7747454	RP11-457M11.5	cis	Skin Sun Exposed Lower leg	GTEx
rs7747454	RP11-457M11.5	cis	Artery Tibial	GTEx
rs7747454	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs7747454	BTN2A1	cis	parietal	SCAN
rs7747454	BTN3A3	cis	cerebellum	SCAN
rs7747454	HIST1H2BM	cis	cerebellum	SCAN
rs7747454	RP11-457M11.5	cis	Heart Left Ventricle	GTEx
rs7747454	HCG11	Cis_1M	lymphoblastoid	RTeQTL
rs7747454	RP11-457M11.5	cis	lung	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27029600-27034400	Weak transcription	GM12878-XiMat	blood
2	chr6:27033400-27034400	Weak transcription	K562	blood
3	chr6:27033800-27035400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:27034000-27034400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:27034000-27034800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr6:27034000-27035000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr6:27034000-27035200	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr6:27034000-27035200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:27034000-27035200	Enhancers	Brain Cingulate Gyrus	brain
10	chr6:27034200-27034400	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr6:27034200-27034400	Enhancers	Brain Hippocampus Middle	brain
12	chr6:27034200-27034400	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr6:27034200-27034400	Active TSS	Brain Substantia Nigra	brain
14	chr6:27034200-27034400	Enhancers	Gastric	stomach
15	chr6:27034200-27034600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr6:27034200-27034600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:27034200-27034600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:27034200-27034600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:27034200-27034600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr6:27034200-27034600	Enhancers	HMEC	breast
21	chr6:27034200-27034800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr6:27034200-27034800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:27034200-27034800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:27034200-27035200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:27034200-27035400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:27034200-27035400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr6:27034200-27035400	Enhancers	Brain Angular Gyrus	brain
28	chr6:27034200-27036000	Enhancers	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links