Variant report

Variant	rs474538
Chromosome Location	chr2:169695196-169695197
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:169685233..169691832-chr2:169692007..169697159,7	K562	blood:
2	chr2:169685233..169688150-chr2:169693345..169695299,2	K562	blood:
3	chr2:169695173..169698676-chr2:169698742..169702914,7	K562	blood:

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10930337	0.85[ASN][1000 genomes]
rs12386224	0.84[ASN][1000 genomes]
rs2177076	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2461386	0.88[ASN][1000 genomes]
rs28675349	0.82[ASN][1000 genomes]
rs2947934	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36083800	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732031	0.87[CHD][hapmap]
rs472233	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs474751	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs487756	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs501303	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs503664	0.96[EUR][1000 genomes]
rs505283	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs508423	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs518337	0.94[EUR][1000 genomes]
rs522893	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs531864	0.83[ASN][1000 genomes]
rs552445	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559113	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578521	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs578797	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs830031	0.82[CHD][hapmap]
rs830194	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs474538	SPC25	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:169676600-169704800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:169676600-169709600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:169683400-169717600	Weak transcription	Ovary	ovary
5	chr2:169688000-169705800	Weak transcription	Psoas Muscle	Psoas
6	chr2:169688000-169710600	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:169688200-169695400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:169690400-169698000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:169692000-169708400	Weak transcription	Colonic Mucosa	Colon
11	chr2:169693200-169707600	Weak transcription	Left Ventricle	heart
12	chr2:169693200-169708400	Weak transcription	Placenta	Placenta
13	chr2:169693400-169699600	Weak transcription	Adipose Nuclei	Adipose
14	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
15	chr2:169693600-169699200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:169693600-169699400	Weak transcription	K562	blood
17	chr2:169693600-169703200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr2:169693600-169707600	Weak transcription	Gastric	stomach
19	chr2:169693600-169711200	Weak transcription	Lung	lung
20	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
21	chr2:169693800-169698000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:169693800-169699600	Weak transcription	Pancreas	Pancrea
23	chr2:169693800-169706800	Weak transcription	Fetal Intestine Large	intestine
24	chr2:169694200-169695400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr2:169694200-169701600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:169694200-169708200	Weak transcription	Fetal Stomach	stomach

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