Variant report

Variant	rs55820305
Chromosome Location	chr1:62456836-62456837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10493313	1.00[ASN][1000 genomes]
rs11207885	0.81[EUR][1000 genomes]
rs11579010	1.00[ASN][1000 genomes]
rs11587128	1.00[ASN][1000 genomes]
rs11588413	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332637	1.00[ASN][1000 genomes]
rs17378995	1.00[ASN][1000 genomes]
rs2016237	1.00[ASN][1000 genomes]
rs2245512	1.00[ASN][1000 genomes]
rs2482857	1.00[ASN][1000 genomes]
rs2499004	1.00[ASN][1000 genomes]
rs2499005	1.00[ASN][1000 genomes]
rs6670989	1.00[ASN][1000 genomes]
rs6681664	1.00[ASN][1000 genomes]
rs6682776	1.00[ASN][1000 genomes]
rs7530070	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518627	chr1:62279594-62517947	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv522020	chr1:62279594-62517947	Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv531876	chr1:62302313-62504349	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
6	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
7	esv2753481	chr1:62424207-62478878	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv546416	chr1:62437872-62492215	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1011197	chr1:62439219-62457712	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv1005178	chr1:62439219-62468653	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv999481	chr1:62439219-62472591	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62385000-62494200	Weak transcription	Aorta	Aorta
2	chr1:62409200-62457000	Weak transcription	Fetal Intestine Large	intestine
3	chr1:62409200-62518600	Weak transcription	Pancreas	Pancrea
4	chr1:62409400-62458400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:62424200-62494200	Weak transcription	Esophagus	oesophagus
6	chr1:62434000-62457000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:62440400-62457000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:62440800-62457000	Weak transcription	Liver	Liver
9	chr1:62441400-62459800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:62442000-62458400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:62444200-62479200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:62446400-62457000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:62446600-62458200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:62446600-62465200	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:62446600-62487600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:62446800-62458200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:62446800-62469400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:62447000-62458200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:62447000-62459000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr1:62447200-62469400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:62447400-62481200	Weak transcription	Lung	lung
22	chr1:62448200-62457200	Weak transcription	Left Ventricle	heart
23	chr1:62448200-62458600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:62448400-62470400	Weak transcription	Ovary	ovary
25	chr1:62448600-62459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:62451800-62457400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:62453400-62460200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:62453600-62461400	Weak transcription	Psoas Muscle	Psoas
29	chr1:62454400-62458000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:62454800-62457200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:62455200-62457000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr1:62455200-62460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr1:62455200-62463000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr1:62455400-62457000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:62455600-62458200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:62455600-62458200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:62456000-62459000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:62456000-62459600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr1:62456200-62478600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:62456400-62458400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:62456600-62459200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:62456800-62457000	Enhancers	Fetal Kidney	kidney
43	chr1:62456800-62457600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr1:62456800-62457600	Enhancers	HMEC	breast
45	chr1:62456800-62459000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr1:62456800-62459000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:62456800-62459600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:62456800-62459800	Enhancers	NHEK	skin

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