Variant report

Variant	rs12538002
Chromosome Location	chr7:6611333-6611334
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	chr7:6611306..6614283-chr7:6628896..6631365,2	MCF-7	breast:
2	chr7:6610972..6612968-chr7:6615946..6618515,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136247	Chromatin interaction
ENSG00000146576	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10235760	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap]
rs10254630	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs10254753	0.93[ASW][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10261986	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10273900	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10276346	0.90[ASN][1000 genomes]
rs10277061	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10279458	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10951987	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10951988	0.93[CHD][hapmap]
rs11559147	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[ASN][1000 genomes]
rs11762346	0.81[CHB][hapmap]
rs11763814	0.85[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs12538197	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12539700	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12669808	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12702529	0.80[ASN][1000 genomes]
rs12702530	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13226346	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1880119	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2346263	0.84[CEU][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap]
rs28541711	0.92[GIH][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3088114	0.81[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs34566172	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3813513	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4075107	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs4272276	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs4512303	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60108089	0.86[EUR][1000 genomes]
rs60742375	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62441317	0.81[EUR][1000 genomes]
rs6952785	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6963775	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6965187	0.84[EUR][1000 genomes]
rs73345000	0.86[ASN][1000 genomes]
rs7776724	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7790874	0.90[JPT][hapmap]
rs7790928	0.82[CEU][hapmap];0.83[JPT][hapmap];0.80[MEX][hapmap]
rs7792808	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7793367	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7793685	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7800917	0.92[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7804036	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9640027	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
3	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
5	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
6	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
7	nsv1020236	chr7:6248930-6690377	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv497874	chr7:6296768-6614902	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv830895	chr7:6514781-6722092	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv887429	chr7:6520676-6659509	Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv887430	chr7:6520676-6668027	Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv508444	chr7:6534110-6700527	Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
13	nsv1025220	chr7:6534278-6736802	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv538717	chr7:6534278-6736802	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
15	nsv887431	chr7:6535517-6690240	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
16	nsv515978	chr7:6535517-6698905	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
17	nsv887432	chr7:6535517-6713985	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
18	nsv887433	chr7:6557135-6668027	Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
19	nsv887434	chr7:6557135-6713985	Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
20	nsv606001	chr7:6563109-6683454	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
21	nsv606002	chr7:6567114-6713985	Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12538002	ZDHHC4	cis	cerebellum	SCAN
rs12538002	GLCCI1	cis	parietal	SCAN
rs12538002	C7orf28B	cis	multi-tissue	Pritchard
rs12538002	AC079742.4	cis	Esophagus Mucosa	GTEx
rs12538002	NXPH1	cis	cerebellum	SCAN
rs12538002	ZDHHC4	cis	Esophagus Mucosa	GTEx
rs12538002	ZDHHC4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6578600-6616200	Weak transcription	Right Atrium	heart
2	chr7:6610200-6612600	Enhancers	HepG2	liver
3	chr7:6610400-6615800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:6610800-6611600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr7:6611000-6611400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:6611200-6611600	Enhancers	GM12878-XiMat	blood
7	chr7:6611200-6611600	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links