Variant report

Variant	rs12987119
Chromosome Location	chr2:11294206-11294207
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:11293490..11296297-chr2:11680693..11684323,3	MCF-7	breast:
2	chr2:11273055..11275301-chr2:11293268..11296881,3	MCF-7	breast:
3	chr2:11292941..11297094-chr2:11480820..11486254,6	MCF-7	breast:
4	chr2:11273067..11276077-chr2:11294167..11297061,3	K562	blood:
5	chr2:11292794..11295094-chr2:11339407..11341727,2	MCF-7	breast:
6	chr2:11271098..11275692-chr2:11293512..11297101,4	MCF-7	breast:
7	chr2:11292916..11295580-chr2:11604494..11607840,3	MCF-7	breast:
8	chr2:11284657..11286652-chr2:11293189..11295227,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264010	Chromatin interaction
ENSG00000169016	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000145063	Chromatin interaction
ENSG00000134318	Chromatin interaction
ENSG00000150873	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10929723	0.86[ASN][1000 genomes]
rs10929724	0.84[ASN][1000 genomes]
rs11676692	0.97[ASN][1000 genomes]
rs11891302	0.81[ASN][1000 genomes]
rs11892387	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11895098	0.80[ASN][1000 genomes]
rs12470798	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12612929	0.86[ASN][1000 genomes]
rs12615623	0.88[ASN][1000 genomes]
rs12994920	0.84[ASN][1000 genomes]
rs12995564	0.84[ASN][1000 genomes]
rs13000987	0.86[ASN][1000 genomes]
rs13022766	0.86[ASN][1000 genomes]
rs13027444	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13028675	0.88[ASN][1000 genomes]
rs13030385	0.88[ASN][1000 genomes]
rs13031027	0.88[ASN][1000 genomes]
rs17366322	0.82[ASN][1000 genomes]
rs1828930	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34315339	0.88[ASN][1000 genomes]
rs34333866	0.86[ASN][1000 genomes]
rs34344767	0.86[ASN][1000 genomes]
rs36026430	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4668715	0.81[ASN][1000 genomes]
rs4668716	0.83[ASN][1000 genomes]
rs4669695	0.87[ASN][1000 genomes]
rs55975936	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6744659	0.86[ASN][1000 genomes]
rs6754718	0.86[ASN][1000 genomes]
rs6754745	0.86[ASN][1000 genomes]
rs71439048	0.86[ASN][1000 genomes]
rs727803	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7581322	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7586305	0.81[ASN][1000 genomes]
rs7601782	0.84[ASN][1000 genomes]
rs7606827	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv520789	chr2:11259067-11312224	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3392188	chr2:11294026-11296874	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12987119	PQLC3	cis	Thyroid	GTEx
rs12987119	PQLC3	cis	lung	GTEx
rs12987119	ROCK2	Cis_1M	lymphoblastoid	RTeQTL
rs12987119	PQLC3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11273600-11294400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr2:11274000-11294600	Weak transcription	Right Atrium	heart
3	chr2:11284600-11294600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:11288200-11294400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:11288200-11294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:11289600-11294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:11289800-11294400	Weak transcription	Pancreas	Pancrea
8	chr2:11291600-11294400	Weak transcription	Adipose Nuclei	Adipose
9	chr2:11291800-11294800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:11292800-11294600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:11294200-11294400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:11294200-11294400	Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr2:11294200-11294400	Bivalent Enhancer	Stomach Smooth Muscle	stomach
14	chr2:11294200-11294400	Flanking Active TSS	Spleen	Spleen
15	chr2:11294200-11294400	Enhancers	Hela-S3	cervix
16	chr2:11294200-11294600	Enhancers	Primary B cells from cord blood	blood
17	chr2:11294200-11294600	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:11294200-11294600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr2:11294200-11294600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:11294200-11294600	Bivalent Enhancer	Fetal Intestine Small	intestine
21	chr2:11294200-11294600	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr2:11294200-11294600	Enhancers	Placenta	Placenta
23	chr2:11294200-11294600	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:11294200-11294800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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