Variant report

Variant	rs12814512
Chromosome Location	chr12:48211506-48211507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48211025-48211560	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:48210800-48213417	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr12:48210061-48213217	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr12:48210923-48215326	Raji	blood:	n/a	n/a
5	MTA3	chr12:48211090-48211664	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:48210746-48211793	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:48210172-48211556	ECC-1	luminal epithelium:	n/a	n/a
8	CTCF	chr12:48211380-48211530	AG04449	skin:	n/a	n/a
9	POLR2A	chr12:48211012-48211568	PANC-1	pancreas:	n/a	n/a
10	CTCF	chr12:48211460-48211610	AG10803	skin:	n/a	n/a
11	POLR2A	chr12:48211288-48212074	K562	blood:	n/a	n/a
12	POLR2A	chr12:48210009-48211562	HUVEC	blood vessel:	n/a	n/a
13	JUN	chr12:48210866-48215048	K562	blood:	n/a	chr12:48212220-48212229 chr12:48212322-48212330 chr12:48214984-48214993 chr12:48212321-48212332
14	CTCF	chr12:48211500-48211650	SK-N-SH_RA	brain:	n/a	n/a
15	POLR2A	chr12:48210763-48214962	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48210893..48211825-chr19:45504374..45505128,2	Hela-S3	cervix:
2	chr1:1550755..1551513-chr12:48210776..48211679,2	Hela-S3	cervix:
3	chr12:48186144..48189155-chr12:48210267..48212702,3	MCF-7	breast:
4	chr12:48191011..48191742-chr12:48211008..48211597,2	MCF-7	breast:

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000272106	Chromatin interaction
ENSG00000104856	Chromatin interaction
ENSG00000197530	Chromatin interaction
ENSG00000061273	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11831940	1.00[CHB][hapmap]
rs2525053	1.00[CHB][hapmap]
rs2525055	0.82[CHB][hapmap]
rs2544029	1.00[CHB][hapmap]
rs2544030	1.00[CHB][hapmap]
rs7958910	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS 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	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12814512	PCGF6	trans	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48205400-48211800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:48207600-48211800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:48208200-48211800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:48208600-48212400	Weak transcription	Ovary	ovary
5	chr12:48209200-48211600	Weak transcription	Aorta	Aorta
6	chr12:48209800-48212400	Enhancers	Fetal Heart	heart
7	chr12:48209800-48212600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
8	chr12:48210000-48211600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:48210000-48212000	Enhancers	Placenta	Placenta
10	chr12:48210000-48212200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:48210000-48212200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr12:48210000-48212400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr12:48210000-48212600	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr12:48210000-48212600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr12:48210000-48212600	Transcr. at gene 5' and 3'	Thymus	Thymus
16	chr12:48210000-48213200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:48210200-48211600	Enhancers	Dnd41	blood
18	chr12:48210200-48211800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:48210200-48211800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:48210200-48211800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:48210200-48211800	Enhancers	Brain Anterior Caudate	brain
22	chr12:48210200-48211800	Flanking Active TSS	Right Ventricle	heart
23	chr12:48210200-48212000	Enhancers	Brain Cingulate Gyrus	brain
24	chr12:48210200-48212200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr12:48210200-48212200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:48210200-48212200	Enhancers	Brain Angular Gyrus	brain
27	chr12:48210200-48212400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr12:48210200-48212400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:48210200-48212400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:48210200-48212400	Enhancers	Fetal Lung	lung
31	chr12:48210200-48212600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:48210200-48212600	Transcr. at gene 5' and 3'	Hela-S3	cervix
33	chr12:48210200-48213000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr12:48210200-48213200	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr12:48210400-48211800	Weak transcription	Fetal Kidney	kidney
36	chr12:48210400-48212200	Flanking Active TSS	Right Atrium	heart
37	chr12:48210400-48212400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:48210400-48212600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:48210600-48211600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
40	chr12:48210600-48211600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr12:48210600-48211600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr12:48210600-48211600	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr12:48210600-48211600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr12:48210600-48211600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr12:48210600-48211800	Flanking Active TSS	Fetal Muscle Leg	muscle
46	chr12:48210600-48211800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr12:48210600-48212000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr12:48210600-48212200	Genic enhancers	Fetal Intestine Small	intestine
49	chr12:48210600-48212400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr12:48210600-48212400	Enhancers	Brain Inferior Temporal Lobe	brain

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