Variant report

Variant	rs12498261
Chromosome Location	chr4:187654362-187654363
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:187652128..187654537-chr4:187654823..187656879,2	MCF-7	breast:
2	chr4:187646992..187648550-chr4:187654225..187656458,2	MCF-7	breast:
3	chr4:187643488..187646584-chr4:187653940..187658823,5	MCF-7	breast:
4	chr4:187651958..187654545-chr4:187671276..187673599,3	K562	blood:
5	chr4:187639395..187641125-chr4:187652205..187654706,2	K562	blood:
6	chr4:187647034..187649598-chr4:187653490..187655513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083857	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2276929	0.96[ASN][1000 genomes]
rs28666848	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57818855	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62342734	1.00[ASN][1000 genomes]
rs73017545	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017551	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7673895	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs960760	0.94[ASN][1000 genomes]
rs960761	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1031603	chr4:187636716-188020741	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187649000-187654800	Weak transcription	Aorta	Aorta
2	chr4:187650400-187655000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr4:187650400-187657000	Weak transcription	HSMM	muscle
4	chr4:187650400-187660800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:187650600-187657000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:187650600-187657000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr4:187650600-187660800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:187650600-187661800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:187651000-187654800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:187651200-187656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr4:187651400-187655000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:187652200-187654800	Weak transcription	A549	lung
13	chr4:187652200-187656800	Weak transcription	Stomach Mucosa	stomach
14	chr4:187652400-187654800	Weak transcription	HepG2	liver
15	chr4:187652400-187655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr4:187652400-187655000	Weak transcription	HMEC	breast
17	chr4:187652400-187655800	Weak transcription	NHEK	skin
18	chr4:187652400-187657000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:187652400-187657200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr4:187652400-187660400	Weak transcription	Fetal Intestine Large	intestine
21	chr4:187652600-187660800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr4:187652800-187655600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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