Variant report

Variant	rs531864
Chromosome Location	chr2:169703660-169703661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:169686945..169689727-chr2:169700154..169704422,5	K562	blood:
2	chr2:169659171..169661687-chr2:169702085..169706270,3	K562	blood:
3	chr2:169702428..169704516-chr2:169706998..169708601,2	K562	blood:
4	chr2:169631455..169632974-chr2:169701424..169703955,2	K562	blood:
5	chr2:169666022..169668624-chr2:169702701..169704508,2	K562	blood:
6	chr2:169700277..169703960-chr2:169704282..169708601,6	K562	blood:
7	chr2:169701436..169703096-chr2:169703453..169705070,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10930337	0.86[ASN][1000 genomes]
rs12386224	0.84[ASN][1000 genomes]
rs2177076	0.86[ASN][1000 genomes]
rs28675349	0.89[ASN][1000 genomes]
rs2947934	0.82[ASN][1000 genomes]
rs474538	0.83[ASN][1000 genomes]
rs474751	0.86[ASN][1000 genomes]
rs481067	0.83[EUR][1000 genomes]
rs487756	0.95[JPT][hapmap]
rs495074	0.85[EUR][1000 genomes]
rs495135	0.86[EUR][1000 genomes]
rs497808	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs501303	0.86[ASN][1000 genomes]
rs505283	0.88[ASN][1000 genomes]
rs508423	0.86[ASN][1000 genomes]
rs526418	0.86[EUR][1000 genomes]
rs531328	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs532779	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs559113	0.87[ASN][1000 genomes]
rs560952	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs578521	0.82[ASN][1000 genomes]
rs578797	0.86[ASN][1000 genomes]
rs830020	0.83[CEU][hapmap];0.85[TSI][hapmap]

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

Variant related diseases (count:1)

Disease	PMID	Source
Mitochondrial DNA levels	25240745	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs531864	SSB	cis	cerebellum	SCAN
rs531864	SPC25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 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	chr2:169699400-169704000	Strong transcription	K562	blood
21	chr2:169702000-169706000	Weak transcription	Pancreas	Pancrea
22	chr2:169702000-169708200	Weak transcription	Fetal Intestine Small	intestine
23	chr2:169702200-169707400	Weak transcription	Adipose Nuclei	Adipose
24	chr2:169702200-169721200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:169702200-169733000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:169702600-169721400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:169702800-169707400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:169703000-169705200	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr2:169703200-169707200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr2:169703200-169713600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr2:169703400-169704000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:169703600-169707000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:169703600-169714600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:169703600-169721200	Weak transcription	GM12878-XiMat	blood

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