Variant report

Variant	rs1370780
Chromosome Location	chr12:104237829-104237830
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr12:104237817-104238609	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:104192525..104200371-chr12:104233987..104238967,10	MCF-7	breast:
2	chr12:104233909..104239694-chr12:104322835..104327398,8	K562	blood:
3	chr12:104234122..104238773-chr12:104347839..104352988,5	MCF-7	breast:

Variant related genes	Relation type
NT5DC3	TF binding region
ENSG00000214198	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000204954	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10735390	0.81[CHD][hapmap]
rs11111809	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1370410	1.00[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370776	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1370784	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805214	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1866069	0.81[CHD][hapmap]
rs1866072	0.81[CHD][hapmap]
rs1992208	0.90[MEX][hapmap]
rs2245322	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255584	0.90[MEX][hapmap]
rs2255791	0.90[MEX][hapmap]
rs2255794	0.90[MEX][hapmap]
rs2255795	0.90[MEX][hapmap]
rs2255797	0.90[MEX][hapmap]
rs2256434	0.93[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2438111	0.90[MEX][hapmap]
rs2576977	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34187551	1.00[AMR][1000 genomes];1.00[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1370780	NT5DC3	cis	multi-tissue	Pritchard
rs1370780	NT5DC3	cis	lymphoblastoid	seeQTL
rs1370780	NT5DC3	cis	parietal	SCAN
rs1370780	GLT8D2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104236000-104238000	Weak transcription	Psoas Muscle	Psoas
2	chr12:104236000-104240800	Weak transcription	NHDF-Ad	bronchial
3	chr12:104236000-104242000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:104236000-104242000	Weak transcription	Pancreas	Pancrea
5	chr12:104236000-104242800	Weak transcription	Aorta	Aorta
6	chr12:104236000-104243000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:104236000-104245000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:104236000-104252600	Weak transcription	Esophagus	oesophagus
9	chr12:104236000-104252600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:104236000-104253600	Weak transcription	Gastric	stomach
11	chr12:104236200-104238200	Weak transcription	HSMMtube	muscle
12	chr12:104236200-104240000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:104236200-104240000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:104236200-104241200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:104236200-104242000	Weak transcription	Fetal Lung	lung
16	chr12:104236200-104242400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:104236200-104246400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:104236400-104245000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:104236400-104246000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:104236600-104241400	Weak transcription	Liver	Liver
21	chr12:104236600-104248400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:104236800-104238400	Enhancers	Fetal Intestine Small	intestine
23	chr12:104237000-104242000	Weak transcription	A549	lung
24	chr12:104237600-104238200	Enhancers	Fetal Intestine Large	intestine
25	chr12:104237600-104238400	Enhancers	Colon Smooth Muscle	Colon
26	chr12:104237600-104238400	Enhancers	Duodenum Mucosa	Duodenum
27	chr12:104237600-104238400	Enhancers	Fetal Heart	heart
28	chr12:104237600-104238400	Enhancers	Small Intestine	intestine

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