Variant report

Variant	rs13139541
Chromosome Location	chr4:85884284-85884285
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:85883700..85885216-chr4:85886284..85888198,2	MCF-7	breast:
2	chr4:85876909..85884375-chr4:85886007..85890757,11	MCF-7	breast:
3	chr4:85840711..85842530-chr4:85882246..85885030,2	MCF-7	breast:
4	chr4:85648671..85650306-chr4:85882299..85884684,2	MCF-7	breast:
5	chr4:85877154..85880144-chr4:85883390..85884959,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163625	Chromatin interaction
ENSG00000180769	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11097028	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500519	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12502559	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503330	0.87[EUR][1000 genomes]
rs13118671	0.86[EUR][1000 genomes]
rs13125323	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13141072	0.86[EUR][1000 genomes]
rs1508670	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17009317	0.83[EUR][1000 genomes]
rs17009334	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35190829	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35892581	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4383611	0.93[EUR][1000 genomes]
rs4590017	0.93[EUR][1000 genomes]
rs4624645	0.81[EUR][1000 genomes]
rs55871210	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55912355	0.89[EUR][1000 genomes]
rs56094216	0.88[EUR][1000 genomes]
rs58074983	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6531783	0.90[EUR][1000 genomes]
rs66965560	0.84[EUR][1000 genomes]
rs67624868	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6815917	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6820517	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71631375	0.90[EUR][1000 genomes]
rs72664928	0.84[EUR][1000 genomes]
rs72664957	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7661609	0.81[EUR][1000 genomes]
rs7682896	0.91[EUR][1000 genomes]
rs7690054	0.93[EUR][1000 genomes]
rs7692223	0.93[EUR][1000 genomes]
rs7694949	0.81[EUR][1000 genomes]
rs7695054	0.86[EUR][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	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv508295	chr4:85822802-85885027	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv879516	chr4:85877561-85895436	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85865200-85886400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:85865800-85885400	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:85866000-85886200	Weak transcription	Fetal Intestine Small	intestine
4	chr4:85866800-85884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:85872000-85886600	Weak transcription	Lung	lung
6	chr4:85873400-85886600	Weak transcription	Esophagus	oesophagus
7	chr4:85873800-85884800	Weak transcription	HSMM	muscle
8	chr4:85873800-85885400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:85873800-85885800	Weak transcription	Osteobl	bone
10	chr4:85874000-85884600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:85874600-85886200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:85876400-85885400	Weak transcription	Left Ventricle	heart
13	chr4:85876600-85885200	Weak transcription	Fetal Brain Male	brain
14	chr4:85877000-85885200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr4:85877400-85886200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr4:85877600-85885200	Weak transcription	Right Atrium	heart
17	chr4:85877600-85885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:85877600-85885400	Weak transcription	Brain Germinal Matrix	brain
19	chr4:85877600-85885400	Weak transcription	Placenta	Placenta
20	chr4:85877600-85885600	Weak transcription	NHEK	skin
21	chr4:85877600-85885800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:85877600-85886000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:85879600-85885200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:85879600-85886200	Weak transcription	Fetal Lung	lung
25	chr4:85879800-85885400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:85879800-85885400	Weak transcription	Aorta	Aorta
27	chr4:85879800-85885800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr4:85879800-85886200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr4:85880000-85885200	Weak transcription	Adipose Nuclei	Adipose
30	chr4:85880000-85885200	Weak transcription	HepG2	liver
31	chr4:85880000-85885400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:85880000-85885400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:85880000-85885400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr4:85880000-85885400	Weak transcription	Fetal Intestine Large	intestine
35	chr4:85880000-85885400	Weak transcription	Gastric	stomach
36	chr4:85880000-85885400	Weak transcription	Pancreas	Pancrea
37	chr4:85880000-85885800	Weak transcription	Fetal Stomach	stomach
38	chr4:85880000-85886000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:85880000-85886200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:85880000-85886200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:85880000-85886200	Weak transcription	NH-A	brain
42	chr4:85880000-85886600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:85880000-85886600	Weak transcription	Spleen	Spleen
44	chr4:85880200-85885800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:85880200-85885800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr4:85880400-85885800	Weak transcription	HUVEC	blood vessel
47	chr4:85880800-85885200	Weak transcription	Fetal Brain Female	brain
48	chr4:85881000-85884800	Weak transcription	Liver	Liver
49	chr4:85881000-85886200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr4:85881400-85885800	Weak transcription	Colon Smooth Muscle	Colon

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