Variant report

Variant	rs7964876
Chromosome Location	chr12:123558705-123558706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123557220..123559958-chr12:123582515..123585405,2	MCF-7	breast:
2	chr12:123547184..123547743-chr12:123557921..123558809,2	MCF-7	breast:
3	chr12:123558228..123559870-chr12:123562881..123566276,3	K562	blood:
4	chr12:123558670..123560288-chr12:123570276..123571928,2	MCF-7	breast:
5	chr12:123557772..123560593-chr12:123574740..123576717,2	K562	blood:
6	chr12:123544563..123545393-chr12:123557820..123558745,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000090975	Chromatin interaction
ENSG00000251497	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12815479	0.82[AMR][1000 genomes]

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	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv832532	chr12:123395927-123573137	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv832533	chr12:123395927-123589290	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv427924	chr12:123412172-123722059	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
6	nsv455732	chr12:123427573-123574838	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv560492	chr12:123427573-123574838	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv560494	chr12:123478378-123560731	Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1042550	chr12:123532028-123659500	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
10	esv3421941	chr12:123556899-123561197	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7964876	CDK2AP1	cis	Esophagus Mucosa	GTEx
rs7964876	LRRC43	cis	cerebellum	SCAN
rs7964876	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs7964876	DDX55	cis	parietal	SCAN
rs7964876	WDR66	cis	parietal	SCAN
rs7964876	TMEM120B	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123542800-123563800	Enhancers	Left Ventricle	heart
2	chr12:123543800-123559000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:123544000-123559000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:123546400-123562400	Enhancers	Liver	Liver
5	chr12:123549600-123561000	Weak transcription	Hela-S3	cervix
6	chr12:123549800-123560000	Weak transcription	Stomach Mucosa	stomach
7	chr12:123550000-123559800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
8	chr12:123550000-123562400	Enhancers	Fetal Heart	heart
9	chr12:123550600-123559400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:123551000-123559000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:123551000-123559200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:123551000-123560200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:123551200-123560400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr12:123551200-123561800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:123553600-123560000	Transcr. at gene 5' and 3'	Thymus	Thymus
16	chr12:123553800-123563800	Enhancers	Right Ventricle	heart
17	chr12:123554000-123559200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr12:123554000-123563000	Enhancers	Right Atrium	heart
19	chr12:123554000-123563800	Enhancers	Brain Hippocampus Middle	brain
20	chr12:123554400-123560400	Enhancers	Colon Smooth Muscle	Colon
21	chr12:123554600-123559000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr12:123555000-123558800	Enhancers	Fetal Brain Female	brain
23	chr12:123555000-123559000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr12:123555000-123559200	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr12:123555200-123560000	Weak transcription	Fetal Intestine Large	intestine
26	chr12:123555600-123559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:123555600-123559000	Enhancers	Fetal Brain Male	brain
28	chr12:123555600-123559400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:123555600-123559600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:123555600-123561200	Weak transcription	Pancreas	Pancrea
31	chr12:123555800-123559600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:123555800-123559800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:123555800-123560000	Weak transcription	Small Intestine	intestine
34	chr12:123555800-123560800	Weak transcription	HUVEC	blood vessel
35	chr12:123555800-123561000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr12:123556000-123559400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:123556000-123559600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:123556000-123559600	Weak transcription	Fetal Intestine Small	intestine
39	chr12:123556000-123559800	Weak transcription	Colonic Mucosa	Colon
40	chr12:123556200-123559000	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr12:123556200-123559600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:123556200-123559600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:123556200-123559800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:123556400-123559400	Weak transcription	Fetal Lung	lung
45	chr12:123556400-123559400	Weak transcription	HMEC	breast
46	chr12:123556400-123559600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:123556400-123561200	Weak transcription	NHLF	lung
48	chr12:123556400-123562600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr12:123556600-123559200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:123556600-123559200	Weak transcription	Placenta Amnion	Placenta Amnion

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