Variant report

Variant	rs3793378
Chromosome Location	chr8:120608983-120608984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:120595191..120597599-chr8:120606307..120609301,2	MCF-7	breast:
2	chr8:120608131..120610098-chr8:120613256..120615439,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11991811	0.82[CEU][hapmap]
rs12676315	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12678907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1374099	0.82[CEU][hapmap]
rs1374100	0.82[CEU][hapmap]
rs17194431	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1992721	0.86[ASW][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2249015	0.83[LWK][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs2289885	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2289888	0.82[CEU][hapmap]
rs2289889	0.82[CEU][hapmap]
rs2326304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2326305	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2326306	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2875906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520196	0.82[CEU][hapmap]
rs4871401	0.82[CEU][hapmap]
rs6469833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6986760	0.82[CEU][hapmap]
rs6987103	0.82[CEU][hapmap]
rs6987232	0.82[CEU][hapmap]
rs7007302	0.82[CEU][hapmap]
rs7012253	0.86[AFR][1000 genomes]
rs7012371	0.86[AFR][1000 genomes]
rs7017581	0.82[CEU][hapmap]
rs7822457	0.82[CEU][hapmap]
rs9297599	0.82[CEU][hapmap]
rs9297600	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868916	chr8:119911943-120762250	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv534028	chr8:120348940-120906079	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv949368	chr8:120568034-121019872	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1021071	chr8:120589963-120968317	Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv891418	chr8:120600965-121301474	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3793378	TAF2	cis	cerebellum	SCAN
rs3793378	ENPP2	cis	multi-tissue	Pritchard

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:120566000-120609200	Weak transcription	Aorta	Aorta
2	chr8:120569600-120613600	Weak transcription	Small Intestine	intestine
3	chr8:120572200-120614200	Weak transcription	Fetal Intestine Large	intestine
4	chr8:120595600-120638000	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:120595800-120633000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:120595800-120637800	Weak transcription	Fetal Stomach	stomach
7	chr8:120597600-120634400	Weak transcription	Fetal Thymus	thymus
8	chr8:120599200-120612800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:120599400-120609000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:120599800-120609800	Weak transcription	Brain Angular Gyrus	brain
11	chr8:120599800-120613600	Weak transcription	Brain Hippocampus Middle	brain
12	chr8:120599800-120614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr8:120600000-120610400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr8:120600000-120617400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr8:120600000-120618000	Weak transcription	Brain Anterior Caudate	brain
16	chr8:120600200-120609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:120601200-120609000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:120601600-120609400	Weak transcription	Brain Substantia Nigra	brain
19	chr8:120601800-120610800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr8:120601800-120614600	Weak transcription	Osteobl	bone
21	chr8:120602000-120613400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:120602000-120614000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr8:120602000-120627000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr8:120602800-120612400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr8:120603000-120613200	Strong transcription	NHDF-Ad	bronchial
26	chr8:120606000-120609000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr8:120606200-120611600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr8:120607000-120614000	Strong transcription	Adipose Nuclei	Adipose
29	chr8:120607200-120609600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr8:120607600-120609000	Strong transcription	Placenta	Placenta
31	chr8:120607800-120613000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr8:120607800-120626600	Weak transcription	Liver	Liver
33	chr8:120608000-120609000	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr8:120608200-120609000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr8:120608200-120609400	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr8:120608200-120610000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr8:120608200-120610000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr8:120608200-120610200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr8:120608400-120611000	Weak transcription	Fetal Lung	lung
40	chr8:120608600-120609000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr8:120608600-120609200	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr8:120608800-120609600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr8:120608800-120610000	Enhancers	H1 Cell Line	embryonic stem cell
44	chr8:120608800-120610000	Enhancers	H9 Cell Line	embryonic stem cell

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