Variant report

Variant	rs56372340
Chromosome Location	chr2:9741536-9741537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495571	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10495572	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10495573	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11676903	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11692112	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11694314	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16867083	0.85[EUR][1000 genomes]
rs17362734	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17362839	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17362902	0.96[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453675	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453724	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17453752	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55883249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57234614	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57407838	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60319753	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs60726087	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119391	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62119392	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119393	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62119422	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62119423	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62119428	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119431	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62119432	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119433	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv214045	chr2:9734039-9742991	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9719200-9747800	Weak transcription	Lung	lung
3	chr2:9732400-9747600	Weak transcription	Placenta	Placenta
4	chr2:9734000-9748000	Weak transcription	Pancreas	Pancrea
5	chr2:9734600-9748000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:9735200-9748400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr2:9735400-9748000	Weak transcription	Aorta	Aorta
8	chr2:9735400-9748000	Weak transcription	Spleen	Spleen
9	chr2:9735600-9748400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:9735800-9747600	Weak transcription	Stomach Mucosa	stomach
11	chr2:9735800-9748200	Weak transcription	Ovary	ovary
12	chr2:9737000-9742600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:9737000-9747800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr2:9737000-9748000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:9737200-9742400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:9737200-9747400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:9737200-9748000	Weak transcription	Small Intestine	intestine
18	chr2:9737400-9747600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:9737400-9747600	Weak transcription	Hela-S3	cervix
20	chr2:9737400-9747800	Weak transcription	Fetal Heart	heart
21	chr2:9737800-9742000	ZNF genes & repeats	Fetal Brain Female	brain
22	chr2:9738000-9742800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
23	chr2:9738200-9741600	ZNF genes & repeats	Fetal Intestine Large	intestine
24	chr2:9738200-9741800	Strong transcription	Fetal Thymus	thymus
25	chr2:9738200-9742800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:9738200-9742800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:9738200-9742800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
28	chr2:9738200-9742800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:9738200-9743400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:9738200-9744400	ZNF genes & repeats	Brain Germinal Matrix	brain
31	chr2:9738400-9741800	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:9738400-9742000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:9738400-9742000	ZNF genes & repeats	GM12878-XiMat	blood
34	chr2:9738400-9742200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr2:9738400-9742400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:9738400-9742800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:9738400-9743000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:9738400-9744800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:9738800-9741800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:9739000-9742000	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr2:9739000-9742000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr2:9739000-9742400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr2:9739200-9742800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
44	chr2:9739200-9747800	Weak transcription	Left Ventricle	heart
45	chr2:9739400-9742000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr2:9739400-9742800	ZNF genes & repeats	Dnd41	blood
47	chr2:9739600-9747800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:9739800-9742800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:9739800-9747600	Weak transcription	Right Ventricle	heart
50	chr2:9739800-9747800	Weak transcription	Psoas Muscle	Psoas

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