Variant report

Variant	rs170425
Chromosome Location	chr4:187825279-187825280
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:187819733..187822489-chr4:187823913..187825517,2	MCF-7	breast:
2	chr4:187646746..187649449-chr4:187824411..187826046,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249539	Chromatin interaction
ENSG00000083857	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11732957	0.88[ASN][1000 genomes]
rs322398	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs322403	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322405	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs322415	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs322416	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs322417	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs322418	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs322423	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs322428	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs322431	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs45359	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv880401	chr4:187668795-188047143	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv1015893	chr4:187768295-188338413	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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
12	nsv537441	chr4:187768295-188338413	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
13	nsv525720	chr4:187792665-188426129	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
14	nsv949342	chr4:187812637-188210592	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv4647	chr4:187820591-187855243	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs170425	RP11-11N5.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187816400-187829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:187821400-187826400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:187821600-187825400	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr4:187821600-187826000	Enhancers	HepG2	liver
5	chr4:187821600-187826200	Enhancers	Adipose Nuclei	Adipose
6	chr4:187821600-187826200	Enhancers	HSMM	muscle
7	chr4:187821600-187826200	Enhancers	HSMMtube	muscle
8	chr4:187821600-187826400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr4:187821600-187826400	Enhancers	NHDF-Ad	bronchial
10	chr4:187821800-187826200	Enhancers	Liver	Liver
11	chr4:187822000-187826200	Enhancers	Stomach Mucosa	stomach
12	chr4:187822400-187825600	Weak transcription	Hela-S3	cervix
13	chr4:187823000-187826200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:187823000-187826200	Enhancers	NHLF	lung
15	chr4:187823400-187825600	Weak transcription	HUVEC	blood vessel
16	chr4:187823600-187826200	Enhancers	Osteobl	bone
17	chr4:187824000-187826200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:187824200-187825400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:187824200-187825600	Weak transcription	Fetal Lung	lung
20	chr4:187824200-187831600	Weak transcription	Fetal Intestine Small	intestine
21	chr4:187824800-187825600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:187824800-187826200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:187824800-187826200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:187824800-187826200	Enhancers	NH-A	brain
25	chr4:187824800-187828800	Weak transcription	Gastric	stomach
26	chr4:187825000-187825800	Flanking Active TSS	A549	lung
27	chr4:187825000-187826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:187825000-187826000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr4:187825000-187826000	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:187825000-187826200	Enhancers	HMEC	breast
31	chr4:187825000-187826200	Enhancers	NHEK	skin
32	chr4:187825000-187827200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:187825200-187825400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:187825200-187825400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:187825200-187826200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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