Variant report

Variant	rs487756
Chromosome Location	chr2:169686559-169686560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:169685233..169688150-chr2:169693345..169695299,2	K562	blood:
2	chr2:169678781..169680698-chr2:169684813..169687488,2	K562	blood:
3	chr2:169685233..169691832-chr2:169692007..169697159,7	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2177076	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2461386	0.83[ASN][1000 genomes]
rs2947934	0.87[ASN][1000 genomes]
rs36083800	0.98[ASN][1000 genomes]
rs3732031	0.82[CHD][hapmap]
rs472233	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs474538	0.92[ASN][1000 genomes]
rs474751	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501303	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs505283	0.88[ASN][1000 genomes]
rs508423	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs511013	0.81[CEU][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs522893	0.98[ASN][1000 genomes]
rs552445	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs559113	0.89[ASN][1000 genomes]
rs578521	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs578797	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs830194	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9287904	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv875381	chr2:169686559-169749841	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs487756	SCN2A	cis	cerebellum	SCAN
rs487756	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169660000-169688200	Weak transcription	Placenta	Placenta
2	chr2:169670000-169698000	Weak transcription	Stomach Mucosa	stomach
3	chr2:169670200-169690200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:169670600-169690800	Weak transcription	Fetal Stomach	stomach
5	chr2:169673400-169687600	Weak transcription	Right Ventricle	heart
6	chr2:169673400-169691600	Weak transcription	Colonic Mucosa	Colon
7	chr2:169673400-169692200	Weak transcription	Gastric	stomach
8	chr2:169676400-169687200	Weak transcription	Adipose Nuclei	Adipose
9	chr2:169676600-169687400	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:169676600-169704800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:169676600-169709600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:169682000-169693600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:169682200-169695000	Weak transcription	Small Intestine	intestine
14	chr2:169683400-169717600	Weak transcription	Ovary	ovary
15	chr2:169684000-169687600	Weak transcription	Lung	lung
16	chr2:169684200-169690200	Weak transcription	Pancreas	Pancrea
17	chr2:169685200-169689000	Strong transcription	Fetal Intestine Large	intestine
18	chr2:169685600-169694200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr2:169685800-169689000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:169686000-169691200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr2:169686000-169693600	Strong transcription	K562	blood
22	chr2:169686200-169687200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:169686400-169687600	Weak transcription	Left Ventricle	heart

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