Variant report

Variant	rs1523609
Chromosome Location	chr7:6535517-6535518
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr7:6535404-6535604	K562	blood:	n/a	n/a
2	RCOR1	chr7:6535301-6535544	K562	blood:	n/a	n/a
3	GATA2	chr7:6534991-6535933	SH-SY5Y	brain:	n/a	chr7:6535718-6535731
4	EP300	chr7:6535506-6535772	SK-N-SH_RA	brain:	n/a	n/a
5	GATA3	chr7:6535095-6535987	SK-N-SH	brain:	n/a	chr7:6535718-6535731
6	FOS	chr7:6535292-6535571	MCF10A-Er-Src	breast:	n/a	n/a
7	MXI1	chr7:6534846-6536362	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr7:6535102-6535917	SH-SY5Y	brain:	n/a	chr7:6535718-6535731
9	GATA3	chr7:6535218-6535856	SK-N-SH	brain:	n/a	chr7:6535718-6535731
10	JUND	chr7:6535253-6535603	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6534685..6537281-chr7:6539803..6541467,2	K562	blood:
2	chr7:6521419..6527137-chr7:6531683..6539786,11	MCF-7	breast:
3	chr7:6485731..6488707-chr7:6533916..6535810,2	K562	blood:
4	chr7:6522302..6524538-chr7:6533835..6535744,2	K562	blood:
5	chr7:6535473..6537831-chr7:6547857..6549421,2	MCF-7	breast:
6	chr7:6533713..6536649-chr7:6538902..6541303,3	K562	blood:

Variant related genes	Relation type
ENSG00000231359	TF binding region
ENSG00000136240	Chromatin interaction
ENSG00000164535	Chromatin interaction
ENSG00000269781	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10951986	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11975679	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.91[AMR][1000 genomes]
rs12113949	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12702519	0.82[CHB][hapmap]
rs13233173	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13239407	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs13240397	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes]
rs1403782	0.87[CHB][hapmap];0.97[GIH][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs2230263	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2347780	0.83[AMR][1000 genomes]
rs4720677	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4724811	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap]
rs4724813	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58885063	0.81[AMR][1000 genomes]
rs6463560	0.81[EUR][1000 genomes]
rs6463561	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes]
rs6463562	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes]
rs6463563	1.00[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs6463564	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap]
rs6463567	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6463568	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945009	1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6953782	0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6959558	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs6959768	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6960903	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6961571	0.87[CHB][hapmap]
rs6964421	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7782950	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7786067	0.93[ASN][1000 genomes]
rs7788091	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7799479	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7800342	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs940243	0.87[CEU][hapmap];0.87[CHB][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	esv1824738	chr7:6431933-6554222	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1825865	chr7:6431933-6554222	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1026878	chr7:6490387-6592374	Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6523800-6536600	Weak transcription	Spleen	Spleen
2	chr7:6527200-6536400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:6529400-6536800	Weak transcription	Esophagus	oesophagus
4	chr7:6529600-6542600	Weak transcription	Right Atrium	heart
5	chr7:6533200-6543000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:6534600-6536600	Weak transcription	Fetal Intestine Small	intestine
7	chr7:6534600-6542400	Weak transcription	Fetal Intestine Large	intestine
8	chr7:6534800-6538200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr7:6534800-6542400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr7:6535000-6535800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:6535000-6535800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:6535000-6535800	Enhancers	Placenta Amnion	Placenta Amnion
13	chr7:6535200-6535600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr7:6535200-6536200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:6535400-6536400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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