Variant report

Variant	rs830031
Chromosome Location	chr2:169669031-169669032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13002530	0.88[ASN][1000 genomes]
rs1568550	0.85[ASN][1000 genomes]
rs17200300	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs3732031	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs830028	0.91[CEU][hapmap];0.94[GIH][hapmap]

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	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv583599	chr2:169664227-169903096	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs830031	SCN2A	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169659800-169672400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:169660000-169676000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:169660000-169688200	Weak transcription	Placenta	Placenta
4	chr2:169661400-169676800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:169662000-169670000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:169662600-169672400	Weak transcription	Gastric	stomach
7	chr2:169662600-169673000	Weak transcription	Left Ventricle	heart
8	chr2:169662600-169675600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:169662800-169669200	Weak transcription	Pancreas	Pancrea
10	chr2:169664400-169672600	Weak transcription	Lung	lung
11	chr2:169667000-169669400	Enhancers	Fetal Intestine Small	intestine
12	chr2:169667000-169671800	Weak transcription	Brain Anterior Caudate	brain
13	chr2:169667800-169670800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr2:169667800-169671600	Weak transcription	Adipose Nuclei	Adipose
15	chr2:169667800-169672800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:169668200-169669200	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr2:169668200-169670000	Enhancers	Ovary	ovary
18	chr2:169668400-169670200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:169668400-169674000	Strong transcription	K562	blood
20	chr2:169668600-169669400	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr2:169668600-169671000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:169668800-169669200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:169668800-169669200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr2:169668800-169670000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:169668800-169670000	Enhancers	Stomach Mucosa	stomach
26	chr2:169668800-169671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:169669000-169669400	Genic enhancers	Fetal Intestine Large	intestine
28	chr2:169669000-169670000	Enhancers	Right Atrium	heart

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