Variant report

Variant	rs12812846
Chromosome Location	chr12:76104853-76104854
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:76032457..76035300-chr12:76104195..76106631,2	MCF-7	breast:
2	chr12:76101934..76108267-chr12:76336185..76339499,5	MCF-7	breast:
3	chr12:76104784..76107360-chr12:76370193..76373274,4	MCF-7	breast:
4	chr12:76092093..76110851-chr12:76415034..76433496,122	MCF-7	breast:
5	chr12:76098446..76100870-chr12:76101330..76106018,5	K562	blood:
6	chr12:76100797..76102905-chr12:76103958..76106069,2	K562	blood:
7	chr12:76102346..76108137-chr12:76108362..76111472,5	MCF-7	breast:
8	chr12:76103874..76111148-chr12:76112002..76118442,8	MCF-7	breast:
9	chr12:76104622..76106937-chr12:76111729..76114237,3	K562	blood:
10	chr12:76015495..76018360-chr12:76104509..76107219,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257453	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000264062	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11180625	0.81[ASN][1000 genomes]
rs11180639	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180640	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11180641	1.00[YRI][hapmap]
rs11180644	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12315800	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12319659	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12822896	1.00[CHD][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs12826237	0.88[ASN][1000 genomes]
rs17115480	0.80[CEU][hapmap]
rs17223072	0.88[ASN][1000 genomes]
rs17223194	0.85[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.86[ASN][1000 genomes]
rs17223651	0.88[ASN][1000 genomes]
rs2367073	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2367074	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34724924	0.92[ASN][1000 genomes]
rs35813830	0.88[ASN][1000 genomes]
rs35881531	1.00[ASN][1000 genomes]
rs7132221	0.90[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71460142	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71460144	0.88[ASN][1000 genomes]
rs7295259	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295484	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295806	0.88[ASN][1000 genomes]
rs7309843	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73124349	0.88[ASN][1000 genomes]
rs7313785	0.90[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7967547	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978873	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

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	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv899314	chr12:76079814-76110751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12812846	FAM164C	trans	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76098400-76105200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:76098800-76105000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:76098800-76114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:76098800-76114400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr12:76099600-76110800	Enhancers	HepG2	liver
6	chr12:76100000-76106800	Weak transcription	Right Ventricle	heart
7	chr12:76100000-76115200	Weak transcription	Pancreas	Pancrea
8	chr12:76100400-76105400	Weak transcription	Psoas Muscle	Psoas
9	chr12:76100400-76106800	Weak transcription	Right Atrium	heart
10	chr12:76100400-76108400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:76100600-76105400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:76100800-76105000	Enhancers	NHDF-Ad	bronchial
13	chr12:76100800-76107000	Weak transcription	Small Intestine	intestine
14	chr12:76101000-76105200	Weak transcription	Stomach Mucosa	stomach
15	chr12:76101000-76106000	Weak transcription	Dnd41	blood
16	chr12:76101000-76106000	Weak transcription	NH-A	brain
17	chr12:76101000-76113600	Weak transcription	Fetal Stomach	stomach
18	chr12:76101400-76114200	Weak transcription	Left Ventricle	heart
19	chr12:76101400-76114800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:76101600-76105400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:76101800-76106000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr12:76101800-76114200	Weak transcription	NHLF	lung
23	chr12:76102200-76106000	Weak transcription	Osteobl	bone
24	chr12:76102600-76106200	Enhancers	A549	lung
25	chr12:76103000-76108000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:76103400-76105200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:76103600-76105400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:76103600-76108800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:76103600-76110200	Enhancers	NHEK	skin
30	chr12:76103600-76115600	Weak transcription	Aorta	Aorta
31	chr12:76103800-76105000	Weak transcription	Esophagus	oesophagus
32	chr12:76103800-76105000	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:76103800-76105000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:76103800-76105400	Weak transcription	Fetal Heart	heart
35	chr12:76104000-76105000	Weak transcription	Fetal Kidney	kidney
36	chr12:76104000-76110600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:76104000-76114400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr12:76104200-76105400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:76104200-76108800	Enhancers	HMEC	breast
40	chr12:76104400-76105600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:76104600-76105400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr12:76104600-76105600	Enhancers	H9 Cell Line	embryonic stem cell
43	chr12:76104600-76105800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr12:76104600-76105800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:76104600-76106000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr12:76104600-76107600	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr12:76104600-76107800	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr12:76104600-76108000	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr12:76104600-76109200	Enhancers	Hela-S3	cervix
50	chr12:76104600-76114200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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