Variant report

Variant	rs56200611
Chromosome Location	chr1:70623530-70623531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70622913..70625686-chr1:70626879..70630763,3	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17131223	0.85[AMR][1000 genomes]
rs17357463	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28537484	0.90[AMR][1000 genomes]
rs3767209	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3767210	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3767211	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41287888	0.86[AMR][1000 genomes]
rs487613	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55634563	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55782523	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55970826	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56297507	0.89[EUR][1000 genomes]
rs61784315	0.86[AMR][1000 genomes]
rs61784317	0.95[AMR][1000 genomes]
rs61784318	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61784319	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61784320	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61785271	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61785280	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61785281	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61785283	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61785284	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61785285	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61785288	0.80[EUR][1000 genomes]
rs6678316	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6696040	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7518536	0.82[AMR][1000 genomes]
rs7552694	0.83[EUR][1000 genomes]
rs7553993	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9970462	0.82[AMR][1000 genomes]
rs9970998	0.82[AMR][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	nsv531879	chr1:70386455-70644617	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005397	chr1:70598803-70634585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	esv1798518	chr1:70604106-70723347	Enhancers Strong transcription Weak transcription Active TSS Flanking 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 miRNA target site	17 gene(s)	inside rSNPs	diseases
4	esv1797140	chr1:70604106-70724622	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv871339	chr1:70605735-70634463	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv870841	chr1:70612416-70696554	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70601000-70643200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr1:70601200-70652000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:70603400-70648800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:70605400-70639400	Weak transcription	Brain Anterior Caudate	brain
5	chr1:70606600-70629600	Weak transcription	Fetal Intestine Small	intestine
6	chr1:70606600-70633800	Weak transcription	Fetal Intestine Large	intestine
7	chr1:70606800-70627800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:70606800-70634800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:70606800-70634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:70606800-70651600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:70606800-70661800	Weak transcription	Brain Hippocampus Middle	brain
12	chr1:70607000-70629600	Weak transcription	Aorta	Aorta
13	chr1:70607000-70633800	Weak transcription	Brain Germinal Matrix	brain
14	chr1:70607000-70670200	Weak transcription	Psoas Muscle	Psoas
15	chr1:70607000-70670400	Weak transcription	Small Intestine	intestine
16	chr1:70607200-70652600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:70607400-70655200	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:70607800-70629200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:70608000-70626800	Weak transcription	Fetal Stomach	stomach
20	chr1:70608200-70645400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:70608400-70653400	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:70608800-70654800	Weak transcription	Thymus	Thymus
23	chr1:70608800-70655800	Weak transcription	Esophagus	oesophagus
24	chr1:70609200-70633800	Weak transcription	Lung	lung
25	chr1:70609200-70647600	Weak transcription	Colonic Mucosa	Colon
26	chr1:70609200-70650200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:70609400-70628200	Weak transcription	Fetal Brain Female	brain
28	chr1:70609400-70638800	Weak transcription	Placenta	Placenta
29	chr1:70609400-70649800	Weak transcription	Fetal Brain Male	brain
30	chr1:70609600-70625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:70609600-70661200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:70610000-70627200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr1:70610000-70642600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:70610000-70656600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:70610000-70667800	Weak transcription	HepG2	liver
36	chr1:70610400-70650200	Weak transcription	GM12878-XiMat	blood
37	chr1:70610400-70653600	Weak transcription	Gastric	stomach
38	chr1:70610600-70669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:70611000-70666600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:70611200-70645000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:70611200-70670400	Weak transcription	Pancreas	Pancrea
42	chr1:70611400-70652800	Weak transcription	Spleen	Spleen
43	chr1:70611600-70643000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:70612400-70669000	Weak transcription	HUVEC	blood vessel
45	chr1:70613000-70649200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:70613400-70638000	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:70613400-70658400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr1:70613600-70657000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:70613600-70667800	Weak transcription	Brain Angular Gyrus	brain
50	chr1:70613800-70623800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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