Variant report

Variant	rs346488
Chromosome Location	chr4:86875253-86875254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:86855497..86859080-chr4:86873833..86876584,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11724681	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs168308	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173201	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182961	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164535	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2164536	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2164537	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2575680	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2589504	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589509	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2665877	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346467	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346471	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs346475	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346478	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs346480	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs346492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs346502	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs346503	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs346504	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs346505	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs346506	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs346507	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35158998	0.82[AMR][1000 genomes]
rs6851229	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs958860	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs958861	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86854000-86893000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:86854200-86880200	Weak transcription	Gastric	stomach
3	chr4:86854200-86893000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr4:86854200-86915800	Weak transcription	Left Ventricle	heart
5	chr4:86858800-86876600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:86862400-86877200	Weak transcription	Liver	Liver
7	chr4:86863600-86902000	Weak transcription	Pancreas	Pancrea
8	chr4:86864000-86877000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:86872400-86875400	Enhancers	HUVEC	blood vessel
10	chr4:86872400-86875600	Strong transcription	Primary B cells from cord blood	blood
11	chr4:86873200-86875800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr4:86873200-86875800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:86873400-86875400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr4:86873400-86875400	Enhancers	Osteobl	bone
15	chr4:86873400-86875600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr4:86873400-86875800	Enhancers	HSMM	muscle
17	chr4:86873600-86875400	Enhancers	HMEC	breast
18	chr4:86874000-86876400	Weak transcription	Fetal Kidney	kidney
19	chr4:86874200-86875400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr4:86874200-86875400	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr4:86874200-86875400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr4:86874200-86875600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr4:86874200-86875800	Enhancers	Fetal Muscle Leg	muscle
24	chr4:86874400-86875600	Enhancers	NHDF-Ad	bronchial
25	chr4:86874400-86875800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:86874400-86876000	Enhancers	Hela-S3	cervix
27	chr4:86874600-86875400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:86874600-86875400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:86874600-86875400	Enhancers	HSMMtube	muscle
30	chr4:86874600-86875600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:86874600-86875600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:86874800-86875400	Flanking Active TSS	A549	lung
33	chr4:86874800-86875600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr4:86875000-86875400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr4:86875000-86875600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:86875000-86876200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr4:86875000-86876600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:86875000-86876600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:86875000-86877000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:86875000-86887200	Weak transcription	Fetal Stomach	stomach
41	chr4:86875000-86891200	Weak transcription	Right Atrium	heart
42	chr4:86875200-86876400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr4:86875200-86876400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:86875200-86876600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr4:86875200-86876800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr4:86875200-86876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr4:86875200-86877600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:86875200-86877800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:86875200-86886800	Weak transcription	Adipose Nuclei	Adipose
50	chr4:86875200-86889000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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