Variant report

Variant	rs560952
Chromosome Location	chr2:169704487-169704488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:169659171..169661687-chr2:169702085..169706270,3	K562	blood:
2	chr2:169702428..169704516-chr2:169706998..169708601,2	K562	blood:
3	chr2:169666022..169668624-chr2:169702701..169704508,2	K562	blood:
4	chr2:169700277..169703960-chr2:169704282..169708601,6	K562	blood:
5	chr2:169701436..169703096-chr2:169703453..169705070,2	K562	blood:

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1467278	0.89[EUR][1000 genomes]
rs2632380	0.96[ASN][1000 genomes]
rs2685799	0.87[ASN][1000 genomes]
rs480731	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488621	0.96[ASN][1000 genomes]
rs493816	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs497808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs506362	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs518337	0.81[ASN][1000 genomes]
rs527393	0.96[ASN][1000 genomes]
rs531328	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs531864	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs540652	0.96[ASN][1000 genomes]
rs543727	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs554494	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs569997	0.96[ASN][1000 genomes]
rs576062	0.94[ASN][1000 genomes]
rs6734923	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7582529	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs830193	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9751269	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9753196	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs560952	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 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	chr2:169693600-169707600	Weak transcription	Gastric	stomach
12	chr2:169693600-169711200	Weak transcription	Lung	lung
13	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
14	chr2:169693800-169706800	Weak transcription	Fetal Intestine Large	intestine
15	chr2:169694200-169708200	Weak transcription	Fetal Stomach	stomach
16	chr2:169698400-169713000	Weak transcription	Fetal Heart	heart
17	chr2:169698400-169721200	Weak transcription	Stomach Mucosa	stomach
18	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:169699000-169706200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr2:169702000-169706000	Weak transcription	Pancreas	Pancrea
21	chr2:169702000-169708200	Weak transcription	Fetal Intestine Small	intestine
22	chr2:169702200-169707400	Weak transcription	Adipose Nuclei	Adipose
23	chr2:169702200-169721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:169702800-169707400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:169703000-169705200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr2:169703200-169707200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:169703200-169713600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:169703600-169707000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:169703600-169714600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:169703600-169721200	Weak transcription	GM12878-XiMat	blood
33	chr2:169704000-169705000	Weak transcription	K562	blood
34	chr2:169704000-169707600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:169704200-169707200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:169704200-169723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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