Variant report

Variant	rs2251367
Chromosome Location	chr1:62602603-62602604
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1811891	0.85[EUR][1000 genomes]
rs2264960	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2457821	0.89[ASN][1000 genomes]
rs2457832	0.82[EUR][1000 genomes]
rs2476195	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2476196	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2476197	0.92[CHB][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2476200	0.82[EUR][1000 genomes]
rs2481667	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481668	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2481669	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481672	0.92[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2481673	0.81[EUR][1000 genomes]
rs2481674	0.84[CHB][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2481675	0.89[ASN][1000 genomes]
rs2481680	0.82[EUR][1000 genomes]
rs2481706	0.82[EUR][1000 genomes]
rs2666468	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2666491	1.00[CHB][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2666493	1.00[CHB][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2666494	0.82[EUR][1000 genomes]
rs2774932	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2984823	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2989012	0.82[EUR][1000 genomes]
rs7520269	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7530787	0.86[EUR][1000 genomes]
rs7535875	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7538266	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9436220	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[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	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
2	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
3	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
4	nsv461650	chr1:62542717-62657530	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv546417	chr1:62542717-62657530	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1012683	chr1:62587852-62643998	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
2	chr1:62536200-62619400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:62545400-62606800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:62548400-62629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:62550200-62607800	Weak transcription	Right Ventricle	heart
6	chr1:62551800-62614000	Weak transcription	Primary T cells from cord blood	blood
7	chr1:62554200-62614000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:62563600-62617400	Weak transcription	Brain Anterior Caudate	brain
9	chr1:62566200-62603400	Weak transcription	Esophagus	oesophagus
10	chr1:62566200-62604400	Weak transcription	Lung	lung
11	chr1:62566200-62614000	Weak transcription	Adipose Nuclei	Adipose
12	chr1:62566800-62608000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:62570200-62607800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:62575200-62608000	Weak transcription	Fetal Kidney	kidney
15	chr1:62576600-62618000	Weak transcription	Psoas Muscle	Psoas
16	chr1:62576800-62607800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:62580000-62611600	Weak transcription	Pancreas	Pancrea
18	chr1:62580200-62617200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:62584600-62603400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:62584600-62607800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:62588600-62622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:62589000-62602800	Weak transcription	NHEK	skin
23	chr1:62590800-62609400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:62593000-62605000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:62593200-62607800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:62593200-62621800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr1:62593400-62617600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:62593600-62636200	Weak transcription	Spleen	Spleen
29	chr1:62593800-62607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr1:62594400-62614800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:62594800-62603000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:62595000-62612600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:62595200-62605200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:62595200-62607600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:62595200-62614200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr1:62595200-62625200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:62595400-62614000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:62595600-62607800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:62595800-62608200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:62596000-62603400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:62596000-62603800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:62596000-62606600	Weak transcription	Fetal Intestine Large	intestine
43	chr1:62596000-62614000	Weak transcription	Left Ventricle	heart
44	chr1:62596000-62617800	Weak transcription	Aorta	Aorta
45	chr1:62596200-62614200	Weak transcription	Ovary	ovary
46	chr1:62597400-62604400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:62598200-62604000	Weak transcription	Liver	Liver
48	chr1:62598400-62604400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:62598400-62604400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:62598600-62603000	Weak transcription	Fetal Stomach	stomach

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