Variant report

Variant	rs7577642
Chromosome Location	chr2:85699750-85699751
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85635544..85709381-chr2:85757395..85791508,633	K562	blood:
2	chr2:85697443..85708380-chr2:85764609..85769775,19	K562	blood:
3	chr2:85695182..85700475-chr2:85771258..85775492,7	K562	blood:
4	chr2:85699337..85700838-chr2:85763015..85764537,2	K562	blood:
5	chr2:85695571..85701406-chr2:85763524..85768199,9	MCF-7	breast:
6	chr2:85671604..85674424-chr2:85697092..85700919,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction
ENSG00000118640	Chromatin interaction
ENSG00000266577	Chromatin interaction
ENSG00000115486	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12613508	0.92[JPT][hapmap]
rs12616455	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs13017730	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1470500	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867881	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4286278	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6714421	0.92[JPT][hapmap]

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	nsv1005351	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv535803	chr2:85242657-85774909	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
3	nsv834283	chr2:85609500-85755708	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Protein quantitative trait loci	18464913	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7577642	RNF103	cis	parietal	SCAN
rs7577642	REEP1	cis	parietal	SCAN
rs7577642	GGCX	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85693400-85701400	Enhancers	Fetal Intestine Small	intestine
2	chr2:85694400-85700600	Enhancers	Fetal Intestine Large	intestine
3	chr2:85695200-85700800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:85696200-85699800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:85696200-85703200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:85696400-85702800	Weak transcription	Left Ventricle	heart
7	chr2:85696400-85703200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:85697600-85699800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr2:85697600-85699800	Enhancers	Stomach Mucosa	stomach
10	chr2:85697600-85700000	Enhancers	Hela-S3	cervix
11	chr2:85697600-85700800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:85697600-85700800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:85697800-85699800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:85697800-85700000	Enhancers	HMEC	breast
15	chr2:85698000-85699800	Enhancers	HSMM	muscle
16	chr2:85698000-85700800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:85698400-85699800	Enhancers	NHDF-Ad	bronchial
18	chr2:85698400-85700400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:85698600-85700000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:85698600-85700200	Enhancers	Muscle Satellite Cultured Cells	--
21	chr2:85698600-85703000	Weak transcription	Colonic Mucosa	Colon
22	chr2:85698600-85705600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:85698800-85699800	Enhancers	Brain Anterior Caudate	brain
24	chr2:85698800-85701000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:85698800-85703200	Weak transcription	Adipose Nuclei	Adipose
26	chr2:85699000-85699800	Enhancers	A549	lung
27	chr2:85699000-85700800	Enhancers	NHEK	skin
28	chr2:85699000-85701600	Enhancers	HepG2	liver
29	chr2:85699000-85702400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:85699000-85703000	Weak transcription	Small Intestine	intestine
31	chr2:85699200-85699800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:85699400-85699800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr2:85699400-85700200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr2:85699400-85700400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:85699400-85700400	Weak transcription	Pancreas	Pancrea
36	chr2:85699400-85702400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:85699400-85703000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:85699400-85703000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr2:85699400-85703000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:85699400-85703000	Weak transcription	Osteobl	bone
41	chr2:85699400-85703200	Weak transcription	Esophagus	oesophagus
42	chr2:85699400-85703200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:85699600-85699800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:85699600-85699800	Weak transcription	Brain Hippocampus Middle	brain
45	chr2:85699600-85700000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr2:85699600-85700000	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:85699600-85700000	Enhancers	HSMMtube	muscle
48	chr2:85699600-85701400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:85699600-85702600	Weak transcription	Liver	Liver

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