Variant report

Variant	rs2576956
Chromosome Location	chr12:104272189-104272190
allele	A/G
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	chr12:104271423..104272333-chr12:104502657..104503502,3	MCF-7	breast:
2	chr12:104266210..104268346-chr12:104271343..104272994,2	K562	blood:
3	chr12:104020008..104020914-chr12:104271652..104272393,3	MCF-7	breast:
4	chr12:104271475..104272300-chr12:104502718..104503322,2	K562	blood:
5	chr12:104270364..104272827-chr12:104323882..104326173,2	K562	blood:
6	chr12:104271327..104273911-chr12:104324205..104326173,2	K562	blood:
7	chr12:104266210..104269616-chr12:104269671..104272994,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000214198	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000166598	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10745981	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10745985	1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861111	1.00[ASN][1000 genomes]
rs11612613	1.00[LWK][hapmap];0.90[MKK][hapmap]
rs1165595	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165671	0.89[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165679	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165683	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12809773	1.00[ASN][1000 genomes]
rs12813601	1.00[ASN][1000 genomes]
rs12819539	1.00[ASN][1000 genomes]
rs12823195	1.00[ASN][1000 genomes]
rs17034955	1.00[ASN][1000 genomes]
rs1866075	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992208	0.83[TSI][hapmap]
rs2255584	0.83[TSI][hapmap]
rs2255791	0.83[TSI][hapmap]
rs2255794	0.83[TSI][hapmap]
rs2255795	0.83[TSI][hapmap]
rs2255797	0.83[TSI][hapmap]
rs2438111	0.83[TSI][hapmap]
rs2576953	1.00[ASN][1000 genomes]
rs2576959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576971	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576976	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2583238	1.00[CEU][hapmap]
rs2722172	0.91[EUR][1000 genomes]
rs2919806	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34309392	1.00[ASN][1000 genomes]
rs34811234	1.00[ASN][1000 genomes]
rs34863477	1.00[ASN][1000 genomes]
rs35392305	1.00[ASN][1000 genomes]
rs35642814	1.00[ASN][1000 genomes]
rs35844634	1.00[ASN][1000 genomes]
rs4964197	1.00[ASN][1000 genomes]
rs57749959	1.00[ASN][1000 genomes]
rs61939568	1.00[ASN][1000 genomes]
rs71466284	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71466286	1.00[ASN][1000 genomes]
rs71466293	1.00[ASN][1000 genomes]
rs73175816	1.00[ASN][1000 genomes]
rs9669259	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9669708	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2576956	MIR3652	cis	Artery Tibial	GTEx
rs2576956	ALDH1L2	cis	parietal	SCAN
rs2576956	MIR3652	cis	Esophagus Muscularis	GTEx
rs2576956	MIR3652	cis	Muscle Skeletal	GTEx
rs2576956	SLC41A2	cis	parietal	SCAN
rs2576956	NT5DC3	cis	parietal	SCAN
rs2576956	GLT8D2	cis	parietal	SCAN
rs2576956	MIR3652	cis	Esophagus Mucosa	GTEx
rs2576956	VSTM2B	trans	cerebellum	SCAN
rs2576956	MIR3652	cis	Adipose Subcutaneous	GTEx
rs2576956	MIR3652	cis	Thyroid	GTEx
rs2576956	MIR3652	cis	Stomach	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104254800-104278200	Weak transcription	Aorta	Aorta
2	chr12:104270000-104272800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:104271400-104272200	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:104271400-104272200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr12:104271400-104272600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:104271600-104274400	Enhancers	GM12878-XiMat	blood
7	chr12:104271800-104272200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr12:104271800-104272200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:104271800-104272200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr12:104271800-104272200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:104271800-104272200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr12:104271800-104272200	Enhancers	Stomach Mucosa	stomach
13	chr12:104271800-104272400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr12:104271800-104272400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:104271800-104272400	Enhancers	Dnd41	blood
16	chr12:104271800-104272600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr12:104271800-104272600	Enhancers	Fetal Thymus	thymus
18	chr12:104271800-104274000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:104271800-104275600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:104272000-104272200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:104272000-104272200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr12:104272000-104272200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr12:104272000-104272200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:104272000-104272200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr12:104272000-104272200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:104272000-104272200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:104272000-104272200	Enhancers	Fetal Intestine Large	intestine
28	chr12:104272000-104272200	Enhancers	Fetal Intestine Small	intestine
29	chr12:104272000-104272200	Enhancers	HUVEC	blood vessel
30	chr12:104272000-104272400	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr12:104272000-104272400	Enhancers	HMEC	breast
32	chr12:104272000-104272400	Enhancers	NHEK	skin
33	chr12:104272000-104273200	Enhancers	HepG2	liver

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