Variant report

Variant	rs17609346
Chromosome Location	chr4:48336371-48336372
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:
2	chr4:48330630..48332591-chr4:48335471..48337148,2	K562	blood:

Variant related genes	Relation type
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10008882	0.82[ASN][1000 genomes]
rs10014431	0.81[ASN][1000 genomes]
rs10033395	0.88[ASN][1000 genomes]
rs10049672	0.84[ASN][1000 genomes]
rs10049857	0.88[ASN][1000 genomes]
rs10517217	0.83[YRI][hapmap]
rs177956	0.81[ASN][1000 genomes]
rs1806833	0.98[ASN][1000 genomes]
rs2036770	0.98[ASN][1000 genomes]
rs4695372	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs58961640	0.98[ASN][1000 genomes]
rs67977239	0.98[ASN][1000 genomes]
rs6830856	0.81[CHB][hapmap];0.98[ASN][1000 genomes]
rs729740	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv275483	chr4:48336371-48338344	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48330000-48342400	Weak transcription	Esophagus	oesophagus
2	chr4:48331000-48336400	Enhancers	NHEK	skin
3	chr4:48331000-48337400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:48331200-48336400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:48331600-48339400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:48331600-48339600	Weak transcription	Stomach Mucosa	stomach
7	chr4:48331600-48340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:48332600-48339200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:48333000-48341800	Weak transcription	A549	lung
10	chr4:48333000-48342400	Weak transcription	Left Ventricle	heart
11	chr4:48333800-48338400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:48334000-48341400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:48334200-48336600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:48334200-48337200	Weak transcription	NHLF	lung
15	chr4:48334200-48339600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:48334200-48340200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:48334200-48342000	Weak transcription	Fetal Heart	heart
18	chr4:48334200-48342000	Weak transcription	HSMM	muscle
19	chr4:48334200-48342200	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr4:48334200-48342600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:48334400-48336800	Weak transcription	HSMMtube	muscle
22	chr4:48334400-48337000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:48334400-48342400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:48334800-48337000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr4:48334800-48341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:48335200-48336800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:48335600-48336800	Enhancers	K562	blood
28	chr4:48335600-48338400	Enhancers	Hela-S3	cervix
29	chr4:48335600-48339600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:48335800-48336400	Enhancers	HMEC	breast
31	chr4:48335800-48342000	Weak transcription	Fetal Kidney	kidney
32	chr4:48336000-48336400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:48336000-48337600	Enhancers	Placenta	Placenta
34	chr4:48336000-48338000	Weak transcription	NHDF-Ad	bronchial
35	chr4:48336200-48336400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:48336200-48336400	Enhancers	Osteobl	bone
37	chr4:48336200-48336800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:48336200-48338200	Enhancers	Psoas Muscle	Psoas

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