Variant report

Variant	rs497808
Chromosome Location	chr2:169705037-169705038
allele	A/C
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	chr2:169700277..169703960-chr2:169704282..169708601,6	K562	blood:
3	chr2:169701436..169703096-chr2:169703453..169705070,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1467278	0.90[EUR][1000 genomes]
rs2632380	0.99[ASN][1000 genomes]
rs2632382	0.81[EUR][1000 genomes]
rs2685799	0.90[ASN][1000 genomes]
rs480731	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs488621	1.00[ASN][1000 genomes]
rs493816	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs506362	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs518337	0.80[ASN][1000 genomes]
rs527393	1.00[ASN][1000 genomes]
rs531328	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs531864	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs540652	1.00[ASN][1000 genomes]
rs543727	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs554494	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs560952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs569997	0.99[ASN][1000 genomes]
rs576062	0.98[ASN][1000 genomes]
rs6734923	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7582529	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs830020	0.83[CHD][hapmap];0.81[TSI][hapmap]
rs830193	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9751269	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9753196	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs497808	SPC25	cis	lymphoblastoid	seeQTL
rs497808	SSB	cis	cerebellum	SCAN
rs497808	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169676600-169709600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:169683400-169717600	Weak transcription	Ovary	ovary
3	chr2:169688000-169705800	Weak transcription	Psoas Muscle	Psoas
4	chr2:169688000-169710600	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:169689000-169721800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:169692000-169708400	Weak transcription	Colonic Mucosa	Colon
7	chr2:169693200-169707600	Weak transcription	Left Ventricle	heart
8	chr2:169693200-169708400	Weak transcription	Placenta	Placenta
9	chr2:169693400-169721400	Weak transcription	Spleen	Spleen
10	chr2:169693600-169707600	Weak transcription	Gastric	stomach
11	chr2:169693600-169711200	Weak transcription	Lung	lung
12	chr2:169693600-169721400	Weak transcription	Right Ventricle	heart
13	chr2:169693800-169706800	Weak transcription	Fetal Intestine Large	intestine
14	chr2:169694200-169708200	Weak transcription	Fetal Stomach	stomach
15	chr2:169698400-169713000	Weak transcription	Fetal Heart	heart
16	chr2:169698400-169721200	Weak transcription	Stomach Mucosa	stomach
17	chr2:169698600-169744600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:169699000-169706200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:169702000-169706000	Weak transcription	Pancreas	Pancrea
20	chr2:169702000-169708200	Weak transcription	Fetal Intestine Small	intestine
21	chr2:169702200-169707400	Weak transcription	Adipose Nuclei	Adipose
22	chr2:169702200-169721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:169702800-169707400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:169703000-169705200	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr2:169703200-169707200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:169703200-169713600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:169703600-169707000	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:169703600-169714600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:169703600-169721200	Weak transcription	GM12878-XiMat	blood
32	chr2:169704000-169707600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:169704200-169707200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:169704200-169723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:169704600-169721400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:169704800-169709800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:169705000-169705200	Enhancers	Fetal Kidney	kidney
38	chr2:169705000-169705200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:169705000-169705400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr2:169705000-169705400	Strong transcription	K562	blood
41	chr2:169705000-169707000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:169705000-169721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:169705000-169723600	Weak transcription	Fetal Brain Female	brain

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