Variant report

Variant	rs12313841
Chromosome Location	chr12:56856618-56856619
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56841419..56844831-chr12:56855069..56859164,5	MCF-7	breast:
2	chr12:56692274..56694985-chr12:56854780..56857399,2	K562	blood:
3	chr12:56855815..56858376-chr12:56867547..56869670,2	MCF-7	breast:
4	chr12:56707286..56709606-chr12:56856082..56858282,2	MCF-7	breast:
5	chr12:56708433..56710457-chr12:56856120..56858915,3	K562	blood:
6	chr12:56752395..56756643-chr12:56855806..56858718,3	K562	blood:
7	chr12:56855046..56856687-chr12:56858307..56861107,2	K562	blood:
8	chr12:56843620..56845384-chr12:56856512..56859341,2	MCF-7	breast:
9	chr12:56855536..56860091-chr12:56860810..56864019,7	MCF-7	breast:
10	chr12:56831181..56832925-chr12:56855832..56858189,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000175336	Chromatin interaction
ENSG00000176422	Chromatin interaction
ENSG00000111602	Chromatin interaction
ENSG00000062485	Chromatin interaction
ENSG00000135517	Chromatin interaction
ENSG00000170581	Chromatin interaction
ENSG00000257727	Chromatin interaction
ENSG00000144785	Chromatin interaction
ENSG00000257303	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11171862	0.90[CEU][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs11171863	0.90[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs11171865	0.85[EUR][1000 genomes]
rs12304519	0.81[CEU][hapmap];0.87[EUR][1000 genomes]
rs12316930	0.85[EUR][1000 genomes]
rs2638318	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2638319	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34287864	0.89[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6581096	0.90[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs71459375	0.84[EUR][1000 genomes]
rs71459376	0.81[EUR][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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv1052713	chr12:56848036-56917602	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12313841	PPP1R1A	cis	parietal	SCAN
rs12313841	RBMS2	Cis_1M	lymphoblastoid	RTeQTL
rs12313841	FUT1	Cis_1M	lymphoblastoid	RTeQTL
rs12313841	CDK4	cis	parietal	SCAN
rs12313841	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL
rs12313841	RBMS2	cis	cerebellum	SCAN
rs12313841	STAC3	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56843800-56858000	Weak transcription	Brain Anterior Caudate	brain
2	chr12:56852200-56861200	Weak transcription	Pancreas	Pancrea
3	chr12:56852800-56856800	Enhancers	HepG2	liver
4	chr12:56853200-56857800	Weak transcription	Stomach Mucosa	stomach
5	chr12:56853400-56858000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:56854400-56858000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:56854600-56857800	Weak transcription	Primary B cells from cord blood	blood
8	chr12:56854800-56857800	Weak transcription	GM12878-XiMat	blood
9	chr12:56855200-56857800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:56855200-56861800	Weak transcription	Placenta	Placenta
11	chr12:56855400-56857800	Weak transcription	K562	blood
12	chr12:56855400-56858000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:56855400-56858000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:56855400-56858000	Weak transcription	NHDF-Ad	bronchial
15	chr12:56855400-56861800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:56855400-56861800	Weak transcription	Osteobl	bone
17	chr12:56855600-56861800	Weak transcription	Right Ventricle	heart
18	chr12:56855800-56857000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:56855800-56857800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:56856000-56858000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr12:56856200-56857000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr12:56856200-56858200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:56856200-56858200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:56856200-56858200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:56856200-56858200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr12:56856200-56858200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr12:56856200-56858200	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:56856400-56856800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr12:56856400-56856800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr12:56856400-56856800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:56856400-56857000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr12:56856400-56858200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:56856600-56856800	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr12:56856600-56856800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:56856600-56857000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:56856600-56857400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:56856600-56858200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr12:56856600-56861200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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