Variant report

Variant	rs10785668
Chromosome Location	chr12:47584431-47584432
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:47498470..47501746-chr12:47583705..47586367,3	MCF-7	breast:
2	chr12:47579225..47581845-chr12:47583061..47584713,2	MCF-7	breast:
3	chr12:47582918..47584527-chr12:47660728..47663353,2	MCF-7	breast:
4	chr12:47583159..47586380-chr12:47586604..47590176,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263838	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10736032	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10748464	0.80[MEX][hapmap]
rs10785664	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10785665	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10881064	0.81[JPT][hapmap]
rs10881066	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10881067	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10881068	0.81[ASN][1000 genomes]
rs10881069	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881070	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10881071	0.85[ASN][1000 genomes]
rs10881072	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183738	1.00[YRI][hapmap]
rs11183750	1.00[YRI][hapmap]
rs11183752	1.00[YRI][hapmap]
rs11183777	1.00[YRI][hapmap]
rs11183783	1.00[YRI][hapmap]
rs12368600	1.00[YRI][hapmap]
rs1404817	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1404818	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554693	1.00[YRI][hapmap]
rs17821774	1.00[YRI][hapmap]
rs1917657	1.00[YRI][hapmap]
rs4768142	1.00[YRI][hapmap]
rs4768143	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768778	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768779	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768781	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768782	1.00[YRI][hapmap]
rs4768783	0.88[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs832741	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10785668	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47578200-47587800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:47580800-47585600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr12:47581000-47585800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:47581800-47584600	Enhancers	Liver	Liver
5	chr12:47581800-47594000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr12:47582000-47585400	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr12:47582200-47584600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:47582200-47584600	Genic enhancers	Primary T cells from cord blood	blood
9	chr12:47582200-47584800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:47582200-47584800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:47582200-47584800	Enhancers	K562	blood
12	chr12:47582200-47585000	Enhancers	NH-A	brain
13	chr12:47582200-47585000	Enhancers	Osteobl	bone
14	chr12:47582200-47585400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:47582200-47585600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:47582400-47584600	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr12:47582400-47584600	Enhancers	Adipose Nuclei	Adipose
18	chr12:47582400-47584600	Enhancers	Duodenum Mucosa	Duodenum
19	chr12:47582400-47584600	Enhancers	Gastric	stomach
20	chr12:47582400-47584600	Enhancers	Spleen	Spleen
21	chr12:47582400-47584800	Enhancers	Left Ventricle	heart
22	chr12:47582400-47584800	Enhancers	HSMM	muscle
23	chr12:47582400-47585200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:47582400-47585400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr12:47582400-47585400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr12:47582400-47585400	Enhancers	NHEK	skin
27	chr12:47582600-47584600	Enhancers	Ovary	ovary
28	chr12:47582600-47584800	Flanking Active TSS	A549	lung
29	chr12:47582600-47585400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:47582800-47584800	Genic enhancers	Primary B cells from cord blood	blood
31	chr12:47582800-47584800	Enhancers	Colon Smooth Muscle	Colon
32	chr12:47582800-47584800	Enhancers	HSMMtube	muscle
33	chr12:47582800-47585000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr12:47582800-47585400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr12:47582800-47585800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr12:47583000-47584800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:47583000-47585800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:47583200-47584800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr12:47583200-47584800	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:47583200-47585000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:47583200-47585000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr12:47583200-47587200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:47583200-47587600	Weak transcription	Pancreas	Pancrea
44	chr12:47583200-47588400	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr12:47583200-47589200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:47583200-47628600	Weak transcription	Aorta	Aorta
47	chr12:47583400-47584600	Enhancers	H9 Cell Line	embryonic stem cell
48	chr12:47583400-47584600	Enhancers	Primary hematopoietic stem cells	blood
49	chr12:47583400-47584800	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:47583400-47585200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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