Variant report

Variant	rs774015
Chromosome Location	chr3:138170116-138170117
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138152067..138153775-chr3:138169983..138172416,2	MCF-7	breast:
2	chr3:138169355..138171117-chr3:138172389..138174530,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158220	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1068685	1.00[CHB][hapmap]
rs10804658	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1091528	1.00[CHB][hapmap]
rs1379257	0.82[CEU][hapmap];0.81[MEX][hapmap]
rs166195	1.00[CHB][hapmap]
rs1673607	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs1679167	0.89[CEU][hapmap]
rs1720836	0.85[CEU][hapmap];0.81[MEX][hapmap]
rs2607795	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs2607796	1.00[CHB][hapmap]
rs2881793	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs361057	1.00[CHB][hapmap]
rs361073	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs361074	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs361075	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs361076	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs361077	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs4678419	0.84[EUR][1000 genomes]
rs484698	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[MEX][hapmap]
rs520904	1.00[CHB][hapmap]
rs523975	1.00[CHB][hapmap]
rs537894	1.00[CHB][hapmap]
rs550507	0.82[CEU][hapmap]
rs559313	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs586946	0.82[CEU][hapmap]
rs600590	1.00[CHB][hapmap]
rs601032	1.00[CHB][hapmap]
rs611134	0.82[CEU][hapmap];0.81[MEX][hapmap]
rs629884	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs643620	1.00[CHB][hapmap]
rs680070	0.82[CEU][hapmap]
rs7625326	0.82[CEU][hapmap]
rs7627685	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs7634745	0.82[CEU][hapmap];0.89[MEX][hapmap]
rs7643973	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs7653815	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs773444	0.82[CEU][hapmap]
rs811322	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap]
rs9811052	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs9817419	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs9848718	0.81[CEU][hapmap]
rs9878436	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv460864	chr3:138100539-138194435	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv591853	chr3:138100539-138194435	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs774015	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs774015	FAIM	cis	lymphoblastoid	seeQTL
rs774015	FAIM	cis	cerebellum	SCAN
rs774015	ESYT3	cis	cerebellum	SCAN
rs774015	FAIM	cis	parietal	SCAN
rs774015	CEP70	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138155000-138182800	Weak transcription	Gastric	stomach
2	chr3:138156000-138175800	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:138156600-138170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:138160600-138170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:138161600-138198400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:138162400-138177200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:138162800-138178800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:138163600-138173800	Weak transcription	Lung	lung
9	chr3:138166600-138183200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:138167800-138171200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:138168600-138171800	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:138169000-138170600	Enhancers	Fetal Muscle Trunk	muscle
13	chr3:138169200-138170400	Weak transcription	Pancreas	Pancrea
14	chr3:138169200-138172400	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr3:138169400-138171600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:138169400-138173800	Weak transcription	Brain Angular Gyrus	brain
17	chr3:138169600-138172400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:138169600-138172400	Enhancers	Placenta	Placenta
19	chr3:138169800-138171000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:138169800-138171200	Enhancers	Spleen	Spleen
21	chr3:138169800-138171400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:138169800-138171800	Enhancers	HMEC	breast
23	chr3:138169800-138174000	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:138170000-138170200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:138170000-138170200	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr3:138170000-138171000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:138170000-138171200	Weak transcription	NHEK	skin
28	chr3:138170000-138171400	Enhancers	HUES6 Cell Line	embryonic stem cell

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