Variant report

Variant	rs309874
Chromosome Location	chr4:48335343-48335344
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	chr4:48329154..48338368-chr4:48340296..48348694,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11732338	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13110483	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13133024	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1472972	0.81[JPT][hapmap]
rs192832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309867	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309869	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs309876	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs309884	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs454707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4599384	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62309397	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482316	chr4:48151953-48338746	Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48336200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
3	chr4:48330800-48336000	Enhancers	NHDF-Ad	bronchial
4	chr4:48331000-48336400	Enhancers	NHEK	skin
5	chr4:48331000-48337400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:48331200-48336400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:48331600-48335600	Weak transcription	K562	blood
8	chr4:48331600-48339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
10	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:48332600-48339200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:48333000-48341800	Weak transcription	A549	lung
13	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
14	chr4:48333800-48338400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:48334200-48335600	Weak transcription	Hela-S3	cervix
17	chr4:48334200-48335600	Weak transcription	Osteobl	bone
18	chr4:48334200-48336600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:48334200-48337200	Weak transcription	NHLF	lung
20	chr4:48334200-48339600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:48334200-48340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
23	chr4:48334200-48342000	Weak transcription	HSMM	muscle
24	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:48334400-48336200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr4:48334400-48336800	Weak transcription	HSMMtube	muscle
28	chr4:48334400-48337000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:48334800-48336200	Weak transcription	Psoas Muscle	Psoas
31	chr4:48334800-48337000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr4:48334800-48341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr4:48335000-48335600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:48335000-48335800	Weak transcription	HMEC	breast
35	chr4:48335000-48336000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr4:48335000-48336000	Weak transcription	Placenta	Placenta
37	chr4:48335200-48336800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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