Variant report

Variant	rs4727445
Chromosome Location	chr7:99639400-99639401
allele	C/T
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99637986..99640124-chr7:99702599..99704667,2	K562	blood:
2	chr7:99636083..99637588-chr7:99637979..99639620,2	K562	blood:
3	chr7:99634010..99640137-chr7:99643841..99648236,8	K562	blood:
4	chr7:99631794..99640933-chr7:99644912..99651639,12	K562	blood:
5	chr7:99633198..99635210-chr7:99638775..99640947,2	K562	blood:
6	chr7:99609453..99615014-chr7:99637646..99644800,9	K562	blood:
7	chr7:99611831..99614044-chr7:99638316..99640846,2	K562	blood:
8	chr7:99613306..99615407-chr7:99637728..99640731,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000221838	Chromatin interaction
ENSG00000106261	Chromatin interaction
ENSG00000166529	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11558475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11558476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531809	0.82[ASN][1000 genomes]
rs12532238	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12673441	0.90[MEX][hapmap];0.93[MKK][hapmap];0.82[ASN][1000 genomes]
rs13238380	0.82[ASN][1000 genomes]
rs2261360	0.90[MEX][hapmap];0.86[MKK][hapmap]
rs2897075	0.82[ASN][1000 genomes]
rs35228488	0.82[ASN][1000 genomes]
rs4308665	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4421299	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4729573	0.81[ASN][1000 genomes]
rs4729575	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs55969052	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56054049	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60697181	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67091024	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67110214	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68038211	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963345	0.82[ASN][1000 genomes]
rs72615158	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72615159	0.82[ASN][1000 genomes]
rs73158411	0.81[ASN][1000 genomes]
rs7780686	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7796006	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7803317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941289	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	esv1824630	chr7:99614770-99639445	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4727445	MCM7	cis	parietal	SCAN
rs4727445	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs4727445	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs4727445	AP4M1	cis	cerebellum	SCAN
rs4727445	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs4727445	MUC17	cis	parietal	SCAN
rs4727445	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs4727445	PILRB	cis	parietal	SCAN
rs4727445	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs4727445	OR2AE1	cis	parietal	SCAN
rs4727445	MBLAC1	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99615400-99639600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr7:99631800-99647000	Weak transcription	Colonic Mucosa	Colon
3	chr7:99632400-99640200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr7:99632600-99646600	Weak transcription	Fetal Heart	heart
5	chr7:99633000-99646600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:99633600-99640200	Weak transcription	Lung	lung
7	chr7:99633600-99641800	Weak transcription	Spleen	Spleen
8	chr7:99633600-99646400	Weak transcription	Pancreas	Pancrea
9	chr7:99633600-99646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:99633600-99646600	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:99633600-99646600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr7:99633600-99646600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:99633600-99646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr7:99633600-99646800	Weak transcription	Psoas Muscle	Psoas
15	chr7:99633600-99647000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:99633800-99646400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr7:99633800-99646400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:99633800-99646600	Weak transcription	Esophagus	oesophagus
19	chr7:99633800-99646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr7:99633800-99647000	Weak transcription	Gastric	stomach
21	chr7:99634000-99646600	Weak transcription	HMEC	breast
22	chr7:99634000-99647000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:99634000-99647000	Weak transcription	Left Ventricle	heart
24	chr7:99634000-99647000	Weak transcription	NHLF	lung
25	chr7:99634200-99646600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:99634200-99647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:99634400-99640200	Enhancers	Liver	Liver
28	chr7:99635000-99640200	Enhancers	HepG2	liver
29	chr7:99635000-99642400	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr7:99635000-99646600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr7:99635000-99646600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr7:99635000-99646800	Weak transcription	HSMMtube	muscle
33	chr7:99635200-99640000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:99635200-99641800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:99635200-99646800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr7:99635200-99646800	Weak transcription	Hela-S3	cervix
37	chr7:99635200-99646800	Weak transcription	NHDF-Ad	bronchial
38	chr7:99635200-99647000	Weak transcription	Ovary	ovary
39	chr7:99635400-99639400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr7:99635400-99646000	Weak transcription	Stomach Mucosa	stomach
41	chr7:99635400-99646800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:99635600-99641800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr7:99635600-99646400	Weak transcription	Fetal Intestine Small	intestine
44	chr7:99635600-99646800	Weak transcription	Thymus	Thymus
45	chr7:99635800-99646600	Weak transcription	Fetal Intestine Large	intestine
46	chr7:99636000-99642200	Weak transcription	NHEK	skin
47	chr7:99636000-99642400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:99636000-99646800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr7:99636000-99646800	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr7:99636200-99639400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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