Variant report

Variant	rs508423
Chromosome Location	chr2:169701054-169701055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:169686945..169689727-chr2:169700154..169704422,5	K562	blood:
2	chr2:169700277..169703960-chr2:169704282..169708601,6	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10930337	0.82[ASN][1000 genomes]
rs12386224	0.81[ASN][1000 genomes]
rs2177076	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461386	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28675349	0.85[ASN][1000 genomes]
rs2947934	0.92[ASN][1000 genomes]
rs36083800	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs472233	0.89[ASN][1000 genomes]
rs474538	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474751	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487756	0.85[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs501303	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505283	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518337	0.82[EUR][1000 genomes]
rs522893	0.89[ASN][1000 genomes]
rs531864	0.86[ASN][1000 genomes]
rs552445	0.89[ASN][1000 genomes]
rs559113	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs578521	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs578797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830194	0.90[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	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
2	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
rs508423	SPC25	Cis_1M	lymphoblastoid	RTeQTL
rs508423	SSB	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169676600-169704800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:169676600-169709600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:169683400-169717600	Weak transcription	Ovary	ovary
4	chr2:169688000-169705800	Weak transcription	Psoas Muscle	Psoas
5	chr2:169688000-169710600	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:169692000-169708400	Weak transcription	Colonic Mucosa	Colon
8	chr2:169693200-169707600	Weak transcription	Left Ventricle	heart
9	chr2:169693200-169708400	Weak transcription	Placenta	Placenta
10	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
11	chr2:169693600-169703200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:169693600-169707600	Weak transcription	Gastric	stomach
13	chr2:169693600-169711200	Weak transcription	Lung	lung
14	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
15	chr2:169693800-169706800	Weak transcription	Fetal Intestine Large	intestine
16	chr2:169694200-169701600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:169694200-169708200	Weak transcription	Fetal Stomach	stomach
18	chr2:169698400-169713000	Weak transcription	Fetal Heart	heart
19	chr2:169698400-169721200	Weak transcription	Stomach Mucosa	stomach
20	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:169699000-169706200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:169699400-169703600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr2:169699400-169704000	Strong transcription	K562	blood
24	chr2:169699600-169702000	Strong transcription	Pancreas	Pancrea
25	chr2:169699600-169702200	Strong transcription	Adipose Nuclei	Adipose
26	chr2:169700200-169701600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:169700400-169702400	Weak transcription	Rectal Mucosa Donor 29	rectum

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