Variant report

Variant	rs12822896
Chromosome Location	chr12:76099541-76099542
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:76098673..76101455-chr12:76339304..76341951,2	MCF-7	breast:
2	chr12:76098446..76100265-chr12:76101330..76104359,3	K562	blood:
3	chr12:76098278..76100434-chr12:76382511..76385380,3	MCF-7	breast:
4	chr12:75919171..75922679-chr12:76098756..76100488,3	MCF-7	breast:
5	chr12:76098571..76100662-chr12:76382454..76384688,2	MCF-7	breast:
6	chr12:76094900..76097140-chr12:76097176..76099734,2	K562	blood:
7	chr12:76092093..76110851-chr12:76415034..76433496,122	MCF-7	breast:
8	chr12:76023357..76025100-chr12:76099295..76101249,2	MCF-7	breast:
9	chr12:76099220..76100944-chr12:76739445..76741568,2	MCF-7	breast:
10	chr12:76098446..76100870-chr12:76101330..76106018,5	K562	blood:
11	chr12:76015734..76021626-chr12:76097256..76101818,9	MCF-7	breast:
12	chr12:76096760..76101934-chr12:76112737..76117926,8	MCF-7	breast:
13	chr12:76098481..76102086-chr12:76423023..76426874,6	MCF-7	breast:
14	chr12:76098765..76099591-chr6:26123921..26124473,2	HCT-116	colon:
15	chr12:76097832..76100387-chr8:102502894..102505190,2	MCF-7	breast:
16	chr12:76097180..76098838-chr12:76099370..76102152,2	MCF-7	breast:
17	chr12:76091616..76093150-chr12:76098574..76100894,2	MCF-7	breast:
18	chr12:76098531..76101496-chr12:76371674..76373378,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257839	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000258088	Chromatin interaction
ENSG00000254024	Chromatin interaction
ENSG00000257453	Chromatin interaction
ENSG00000139289	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000083307	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11180624	0.90[ASN][1000 genomes]
rs11180625	0.93[ASN][1000 genomes]
rs11180639	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11180640	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11180644	0.86[MEX][hapmap];0.83[ASN][1000 genomes]
rs12315800	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12319659	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12812846	1.00[CHD][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs12826237	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223072	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17223194	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17223651	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2367073	1.00[ASN][1000 genomes]
rs2367074	1.00[ASN][1000 genomes]
rs34724924	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35094428	0.90[ASN][1000 genomes]
rs35813830	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35881531	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67943440	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7132221	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71460142	1.00[ASN][1000 genomes]
rs71460144	1.00[ASN][1000 genomes]
rs7295259	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7295484	1.00[ASN][1000 genomes]
rs7295806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7309843	1.00[CHB][hapmap]
rs73124349	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313785	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7967547	0.95[ASN][1000 genomes]

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	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
rs12822896	E2F7	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:76079400-76099800	Weak transcription	Right Atrium	heart
2	chr12:76084600-76099600	Weak transcription	Pancreas	Pancrea
3	chr12:76088800-76100600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:76089000-76100600	Weak transcription	HMEC	breast
5	chr12:76089600-76099800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:76089600-76100200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:76089600-76100400	Weak transcription	NHEK	skin
8	chr12:76094200-76100200	Weak transcription	Psoas Muscle	Psoas
9	chr12:76095400-76100000	Weak transcription	Adipose Nuclei	Adipose
10	chr12:76096000-76100600	Weak transcription	Left Ventricle	heart
11	chr12:76097000-76099600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:76097000-76101000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr12:76097200-76100400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr12:76097400-76099800	Weak transcription	Dnd41	blood
15	chr12:76097600-76099600	Enhancers	HUVEC	blood vessel
16	chr12:76097800-76101000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr12:76098000-76100000	Enhancers	K562	blood
18	chr12:76098000-76100400	Enhancers	Fetal Heart	heart
19	chr12:76098000-76100800	Enhancers	Fetal Kidney	kidney
20	chr12:76098200-76101000	Enhancers	Fetal Stomach	stomach
21	chr12:76098200-76104000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:76098400-76104600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:76098400-76105200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:76098600-76099800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:76098600-76100400	Enhancers	NHDF-Ad	bronchial
26	chr12:76098600-76101000	Enhancers	HSMM	muscle
27	chr12:76098600-76101800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:76098800-76099600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:76098800-76099600	Weak transcription	HepG2	liver
30	chr12:76098800-76099800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:76098800-76099800	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:76098800-76100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr12:76098800-76104600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:76098800-76105000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:76098800-76114200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:76098800-76114400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:76099000-76099600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr12:76099200-76101000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:76099200-76101800	Enhancers	NHLF	lung
40	chr12:76099200-76102200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:76099400-76099600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:76099400-76099600	Enhancers	A549	lung
43	chr12:76099400-76099800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:76099400-76099800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:76099400-76099800	Enhancers	Hela-S3	cervix
46	chr12:76099400-76100200	Enhancers	Osteobl	bone
47	chr12:76099400-76100400	Enhancers	H9 Cell Line	embryonic stem cell
48	chr12:76099400-76100400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:76099400-76100600	Enhancers	Stomach Smooth Muscle	stomach
50	chr12:76099400-76100800	Enhancers	Colon Smooth Muscle	Colon

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