Variant report

Variant	rs522893
Chromosome Location	chr2:169690729-169690730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:169653689..169656123-chr2:169689883..169693287,3	K562	blood:
2	chr2:169682202..169684023-chr2:169687028..169690817,4	K562	blood:
3	chr2:169685233..169691832-chr2:169692007..169697159,7	K562	blood:

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12386224	0.80[ASN][1000 genomes]
rs17200300	0.80[CHB][hapmap]
rs2177076	0.89[ASN][1000 genomes]
rs2461386	0.82[ASN][1000 genomes]
rs2555932	0.80[EUR][1000 genomes]
rs2947934	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36083800	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732031	0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs472233	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474538	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs474751	0.89[ASN][1000 genomes]
rs487756	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs490278	0.83[GIH][hapmap];0.80[EUR][1000 genomes]
rs501303	0.89[ASN][1000 genomes]
rs503664	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs505283	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs508423	0.89[ASN][1000 genomes]
rs518337	0.92[EUR][1000 genomes]
rs552445	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs559113	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578521	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs578797	0.89[ASN][1000 genomes]
rs73032206	0.80[ASN][1000 genomes]
rs830027	0.80[EUR][1000 genomes]
rs830029	0.80[EUR][1000 genomes]
rs830194	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862638	0.80[EUR][1000 genomes]
rs9287904	0.84[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
rs522893	SPC25	Cis_1M	lymphoblastoid	RTeQTL
rs522893	SCN2A	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169670000-169698000	Weak transcription	Stomach Mucosa	stomach
2	chr2:169670600-169690800	Weak transcription	Fetal Stomach	stomach
3	chr2:169673400-169691600	Weak transcription	Colonic Mucosa	Colon
4	chr2:169673400-169692200	Weak transcription	Gastric	stomach
5	chr2:169676600-169704800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:169676600-169709600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:169682000-169693600	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr2:169682200-169695000	Weak transcription	Small Intestine	intestine
9	chr2:169683400-169717600	Weak transcription	Ovary	ovary
10	chr2:169685600-169694200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr2:169686000-169691200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr2:169686000-169693600	Strong transcription	K562	blood
13	chr2:169687800-169692800	Weak transcription	Right Ventricle	heart
14	chr2:169688000-169691800	Weak transcription	Left Ventricle	heart
15	chr2:169688000-169693400	Strong transcription	Adipose Nuclei	Adipose
16	chr2:169688000-169705800	Weak transcription	Psoas Muscle	Psoas
17	chr2:169688000-169710600	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:169688200-169690800	Strong transcription	Placenta	Placenta
19	chr2:169688200-169695400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:169688400-169692600	Weak transcription	Lung	lung
21	chr2:169689000-169691800	Weak transcription	Fetal Intestine Large	intestine
22	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:169689200-169694200	Strong transcription	Fetal Intestine Small	intestine
24	chr2:169690200-169693600	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:169690200-169693800	Strong transcription	Pancreas	Pancrea
26	chr2:169690400-169698000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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