Variant report

Variant	rs9357004
Chromosome Location	chr6:26303319-26303320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26298226..26302265-chr6:26302450..26306372,5	MCF-7	breast:
2	chr6:26295061..26296606-chr6:26303262..26305423,2	MCF-7	breast:
3	chr6:26303134..26304792-chr6:26569480..26571384,2	K562	blood:
4	chr21:15862079..15863579-chr6:26301955..26303620,2	K562	blood:
5	chr6:26302784..26306678-chr6:27115101..27117837,4	K562	blood:
6	chr6:26295520..26298937-chr6:26299189..26303889,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1124999	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1125000	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12526215	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2142703	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2179152	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2393592	0.85[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs2393593	0.80[CEU][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs34916901	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35310879	0.80[EUR][1000 genomes]
rs3999544	0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs4145910	1.00[JPT][hapmap]
rs4412192	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6456712	0.81[EUR][1000 genomes]
rs6916289	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6931391	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6939589	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6940237	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7450556	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs766406	1.00[JPT][hapmap]
rs766407	1.00[JPT][hapmap]
rs7746807	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7747133	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7748935	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7761298	0.87[EUR][1000 genomes]
rs7769028	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7771202	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9358915	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9358917	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9358919	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9366649	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs9366651	0.86[EUR][1000 genomes]
rs9379838	0.87[EUR][1000 genomes]
rs9379843	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393690	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9393692	0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs9393693	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9393694	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9467703	0.90[CHD][hapmap];1.00[JPT][hapmap]
rs989134	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
6	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
7	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases
8	nsv1015782	chr6:26026870-26323895	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1114 gene(s)	inside rSNPs	diseases
9	nsv1018665	chr6:26026870-26352046	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1116 gene(s)	inside rSNPs	diseases
10	nsv601173	chr6:26239404-26322524	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	184 gene(s)	inside rSNPs	diseases
11	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9357004	HIST1H4H	cis	multi-tissue	Pritchard
rs9357004	HIST1H4E	cis	multi-tissue	Pritchard
rs9357004	HIST1H3H	cis	parietal	SCAN
rs9357004	HIST1H4F	cis	parietal	SCAN
rs9357004	BTN3A2	cis	lymphoblastoid	seeQTL
rs9357004	BTN3A3	cis	lymphoblastoid	seeQTL
rs9357004	ACOT13	cis	cerebellum	SCAN
rs9357004	HIST1H2BD	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26297600-26304400	Weak transcription	NHLF	lung
2	chr6:26297800-26304800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:26297800-26305000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:26298000-26305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:26301200-26304800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:26301400-26304600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:26301400-26305000	Weak transcription	NHDF-Ad	bronchial
8	chr6:26302600-26304400	Weak transcription	GM12878-XiMat	blood
9	chr6:26303200-26303600	Enhancers	K562	blood
10	chr6:26303200-26303800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:26303200-26305000	Enhancers	HepG2	liver

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