Variant report

Variant	rs56192500
Chromosome Location	chr2:85882919-85882920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85763539..85766353-chr2:85881297..85884242,2	K562	blood:

Variant related genes	Relation type
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11891495	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12463933	0.89[ASN][1000 genomes]
rs1374370	0.80[ASN][1000 genomes]
rs14976	0.83[ASN][1000 genomes]
rs17508843	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289976	0.83[ASN][1000 genomes]
rs2304566	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34623563	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62166770	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62166779	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72843872	0.83[ASN][1000 genomes]
rs7607208	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874459	chr2:85828014-85939207	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv874460	chr2:85828014-85941074	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv874461	chr2:85853653-85939207	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv874462	chr2:85853653-85941074	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874463	chr2:85853653-85946708	Strong transcription Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56192500	VAMP5	Cis_1M	lymphoblastoid	RTeQTL
rs56192500	VAMP5	cis	Esophagus Mucosa	GTEx
rs56192500	VAMP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85845000-85883600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:85845400-85886400	Strong transcription	Fetal Muscle Leg	muscle
3	chr2:85846000-85887000	Strong transcription	Liver	Liver
4	chr2:85846000-85887400	Strong transcription	Fetal Intestine Small	intestine
5	chr2:85846200-85889400	Strong transcription	Thymus	Thymus
6	chr2:85861600-85883800	Strong transcription	HMEC	breast
7	chr2:85862000-85887200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:85865000-85884000	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:85873200-85886600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:85876400-85888800	Weak transcription	Fetal Heart	heart
11	chr2:85876400-85888800	Weak transcription	Right Atrium	heart
12	chr2:85876600-85885000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:85876600-85895400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:85877000-85889000	Weak transcription	Stomach Mucosa	stomach
15	chr2:85877000-85890000	Weak transcription	Ovary	ovary
16	chr2:85877200-85883000	Weak transcription	Right Ventricle	heart
17	chr2:85877200-85884800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr2:85877200-85885200	Weak transcription	Brain Angular Gyrus	brain
19	chr2:85877200-85888600	Weak transcription	Aorta	Aorta
20	chr2:85877200-85893200	Weak transcription	Brain Substantia Nigra	brain
21	chr2:85877800-85890200	Weak transcription	Small Intestine	intestine
22	chr2:85878200-85885200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr2:85878200-85886400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:85878200-85888800	Weak transcription	Brain Anterior Caudate	brain
25	chr2:85878600-85886200	Weak transcription	Esophagus	oesophagus
26	chr2:85878800-85886600	Weak transcription	Gastric	stomach
27	chr2:85878800-85891400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:85879400-85883200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr2:85879400-85883200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:85879400-85885200	Weak transcription	Fetal Brain Male	brain
31	chr2:85879400-85888000	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:85879400-85889200	Weak transcription	Colonic Mucosa	Colon
33	chr2:85879400-85890200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:85879400-85890200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:85879600-85883400	Weak transcription	Hela-S3	cervix
36	chr2:85879600-85885200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:85879600-85885800	Weak transcription	Spleen	Spleen
38	chr2:85879600-85887000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:85879600-85889800	Weak transcription	Fetal Intestine Large	intestine
40	chr2:85879600-85894000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr2:85879600-85896000	Weak transcription	GM12878-XiMat	blood
42	chr2:85879800-85883200	Weak transcription	Lung	lung
43	chr2:85879800-85883200	Weak transcription	HSMMtube	muscle
44	chr2:85879800-85883400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:85879800-85884800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:85879800-85888600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:85880000-85883000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:85880000-85883000	Weak transcription	Fetal Lung	lung
49	chr2:85880000-85883000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:85880000-85883000	Strong transcription	HSMM	muscle

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