Variant report

Variant	rs28685817
Chromosome Location	chr5:60597622-60597623
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:60586340..60593423-chr5:60595007..60600646,11	MCF-7	breast:
2	chr5:60596613..60601643-chr5:60625817..60629986,6	MCF-7	breast:
3	chr5:60456737..60461436-chr5:60596585..60603587,8	MCF-7	breast:
4	chr5:60593618..60596553-chr5:60596973..60598822,2	K562	blood:
5	chr5:60595162..60604481-chr5:60621758..60631019,20	MCF-7	breast:
6	chr5:60457408..60460091-chr5:60596786..60599332,3	MCF-7	breast:
7	chr5:60595107..60599156-chr5:60625279..60628331,4	K562	blood:
8	chr5:60588266..60590443-chr5:60596275..60598423,2	MCF-7	breast:
9	chr5:60596572..60599250-chr5:60605731..60609279,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10044518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10044575	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12188621	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188882	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4256302	1.00[ASN][1000 genomes]
rs4382119	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4452517	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59628996	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105361	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73105363	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
2	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60594000-60602400	Enhancers	NHDF-Ad	bronchial
2	chr5:60594000-60602800	Enhancers	HMEC	breast
3	chr5:60594400-60599200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr5:60595000-60599600	Weak transcription	Fetal Thymus	thymus
5	chr5:60595400-60597800	Enhancers	NHEK	skin
6	chr5:60595400-60598800	Weak transcription	Ovary	ovary
7	chr5:60596000-60598400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr5:60596400-60598000	Enhancers	HSMM	muscle
9	chr5:60596400-60598000	Enhancers	NH-A	brain
10	chr5:60596400-60598600	Enhancers	Brain Germinal Matrix	brain
11	chr5:60596800-60601800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:60597000-60597800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:60597000-60597800	Enhancers	HSMMtube	muscle
14	chr5:60597000-60598000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:60597000-60598000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr5:60597000-60598800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:60597000-60599000	Enhancers	Fetal Heart	heart
18	chr5:60597000-60599000	Enhancers	Fetal Intestine Large	intestine
19	chr5:60597000-60599200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:60597000-60599600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:60597000-60605000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:60597200-60597800	Enhancers	H1 Cell Line	embryonic stem cell
23	chr5:60597200-60598000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:60597200-60598000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr5:60597200-60598000	Enhancers	Esophagus	oesophagus
26	chr5:60597200-60598200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:60597200-60598200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr5:60597200-60598200	Enhancers	Left Ventricle	heart
29	chr5:60597200-60598200	Enhancers	Right Atrium	heart
30	chr5:60597200-60598200	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr5:60597200-60598400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr5:60597200-60598400	Enhancers	HUVEC	blood vessel
33	chr5:60597200-60598600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:60597200-60598600	Enhancers	Brain Substantia Nigra	brain
35	chr5:60597200-60598600	Flanking Active TSS	HepG2	liver
36	chr5:60597200-60598800	Enhancers	Fetal Intestine Small	intestine
37	chr5:60597200-60598800	Enhancers	Fetal Muscle Leg	muscle
38	chr5:60597200-60598800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr5:60597200-60598800	Enhancers	Stomach Mucosa	stomach
40	chr5:60597200-60599000	Enhancers	Placenta	Placenta
41	chr5:60597200-60599200	Enhancers	Brain Hippocampus Middle	brain
42	chr5:60597200-60599200	Enhancers	Colon Smooth Muscle	Colon
43	chr5:60597200-60599200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr5:60597200-60599800	Enhancers	Adipose Nuclei	Adipose
45	chr5:60597200-60599800	Enhancers	Placenta Amnion	Placenta Amnion
46	chr5:60597400-60597800	Enhancers	H9 Cell Line	embryonic stem cell
47	chr5:60597400-60597800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr5:60597400-60598000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:60597400-60598000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:60597400-60598200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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