Variant report

Variant	rs4767664
Chromosome Location	chr12:118537679-118537680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:118536275..118537815-chr12:118538077..118540227,2	MCF-7	breast:
2	chr12:118497389..118502867-chr12:118535601..118543920,23	MCF-7	breast:
3	chr12:118492994..118495394-chr12:118535946..118537983,2	MCF-7	breast:
4	chr12:118498416..118504096-chr12:118537510..118543393,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176871	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10850960	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10850961	0.85[ASN][1000 genomes]
rs11068822	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11068826	0.81[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11068830	0.85[ASN][1000 genomes]
rs11830698	0.83[ASN][1000 genomes]
rs4590911	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs6490167	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6490168	0.85[ASN][1000 genomes]
rs7314781	0.86[ASN][1000 genomes]
rs7978165	0.86[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7980628	0.85[JPT][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv560389	chr12:118502467-118564087	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv899546	chr12:118515230-118563982	Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4767664	VSIG10	cis	Artery Tibial	GTEx
rs4767664	CCDC64	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118500800-118539600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:118500800-118539800	Weak transcription	Right Ventricle	heart
3	chr12:118500800-118540800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr12:118501000-118539600	Weak transcription	Psoas Muscle	Psoas
5	chr12:118501000-118540200	Weak transcription	HUVEC	blood vessel
6	chr12:118501000-118540800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr12:118501000-118540800	Weak transcription	NH-A	brain
8	chr12:118501200-118540400	Weak transcription	Brain Germinal Matrix	brain
9	chr12:118501200-118540800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:118501200-118541000	Weak transcription	Aorta	Aorta
11	chr12:118501600-118540400	Weak transcription	NHLF	lung
12	chr12:118502200-118540800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:118502200-118540800	Weak transcription	Brain Anterior Caudate	brain
14	chr12:118509000-118538400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:118511800-118539600	Weak transcription	Pancreas	Pancrea
16	chr12:118514600-118540400	Weak transcription	Fetal Heart	heart
17	chr12:118515800-118540800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:118515800-118540800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:118516000-118539800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:118517600-118540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:118517600-118540800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:118517600-118540800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:118518600-118540000	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:118518600-118540800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:118519000-118540400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:118519000-118540800	Weak transcription	Colon Smooth Muscle	Colon
27	chr12:118519200-118539800	Weak transcription	Left Ventricle	heart
28	chr12:118519400-118540600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr12:118519600-118540200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:118520200-118540600	Weak transcription	Liver	Liver
31	chr12:118528000-118540400	Weak transcription	Dnd41	blood
32	chr12:118528800-118539800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:118528800-118540400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:118528800-118540800	Weak transcription	Lung	lung
35	chr12:118529000-118540000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:118529000-118540600	Weak transcription	Spleen	Spleen
37	chr12:118529600-118540800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:118530400-118540400	Weak transcription	Fetal Lung	lung
39	chr12:118532000-118540400	Weak transcription	Ovary	ovary
40	chr12:118532400-118540000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:118532600-118540800	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:118533600-118539600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr12:118533600-118539800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:118533600-118540000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:118533600-118540000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:118533600-118540200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:118533600-118540400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:118533600-118540400	Weak transcription	Fetal Stomach	stomach
49	chr12:118536000-118539600	Weak transcription	Colonic Mucosa	Colon
50	chr12:118536400-118538400	Weak transcription	H1 Cell Line	embryonic stem cell

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