Variant report

Variant	rs56966204
Chromosome Location	chr12:9260439-9260440
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	chr12:9258445-9260736	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9258660-9260722	HepG2	liver:	n/a	n/a
3	HEY1	chr12:9258672-9260708	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9258586-9260734	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9259417-9260439	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:9250026-9260702	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:9258361-9262806	HepG2	liver:	n/a	n/a
8	MBD4	chr12:9253090-9260788	HepG2	liver:	n/a	n/a
9	MYBL2	chr12:9259883-9260625	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:9259132-9262510	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:9252994-9260800	HepG2	liver:	n/a	n/a
12	MBD4	chr12:9259408-9260680	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9256413..9259113-chr12:9259461..9261361,2	K562	blood:

Variant related genes	Relation type
A2M	TF binding region
ENSG00000175899	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16917975	1.00[AMR][1000 genomes]
rs16918033	1.00[AMR][1000 genomes]
rs16918120	1.00[AMR][1000 genomes]
rs16918292	1.00[AMR][1000 genomes]
rs1805748	1.00[AMR][1000 genomes]
rs1805764	1.00[AMR][1000 genomes]
rs1805769	1.00[AMR][1000 genomes]
rs58537365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59792548	1.00[AMR][1000 genomes]
rs60190629	1.00[AMR][1000 genomes]
rs7297635	1.00[AMR][1000 genomes]
rs7304882	1.00[AMR][1000 genomes]
rs74060300	1.00[AMR][1000 genomes]
rs74060302	1.00[AMR][1000 genomes]
rs74060475	1.00[AMR][1000 genomes]
rs74060477	1.00[AMR][1000 genomes]
rs74060491	1.00[AMR][1000 genomes]
rs74061403	1.00[AMR][1000 genomes]
rs74061408	1.00[AMR][1000 genomes]
rs74061444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7980046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	esv3504674	chr12:9243858-9318016	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3502154	chr12:9243906-9317851	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3502155	chr12:9243906-9317851	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3504685	chr12:9243948-9317959	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv527404	chr12:9250601-9435244	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
2	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
3	chr12:9232200-9264600	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:9237200-9261200	Strong transcription	Liver	Liver
6	chr12:9237200-9265200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:9237400-9264200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:9238600-9265800	Strong transcription	Skeletal Muscle Female	skeletal muscle
9	chr12:9239400-9262800	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:9239400-9264000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:9239600-9265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:9240800-9267600	Weak transcription	Fetal Intestine Large	intestine
13	chr12:9241200-9262800	Strong transcription	Adipose Nuclei	Adipose
14	chr12:9241600-9264000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:9243000-9274800	Weak transcription	Small Intestine	intestine
16	chr12:9243400-9265400	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:9244200-9265200	Weak transcription	Brain Anterior Caudate	brain
18	chr12:9245000-9266000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:9246200-9265200	Weak transcription	Fetal Brain Male	brain
20	chr12:9246600-9266000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:9246600-9268600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:9248000-9262600	Strong transcription	Left Ventricle	heart
23	chr12:9249400-9268800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:9249600-9267600	Weak transcription	HSMMtube	muscle
25	chr12:9250000-9262800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr12:9250600-9268200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:9250600-9268600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:9251000-9266000	Weak transcription	NHLF	lung
29	chr12:9251200-9264800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr12:9251400-9268200	Weak transcription	Pancreas	Pancrea
31	chr12:9252200-9265200	Weak transcription	Colonic Mucosa	Colon
32	chr12:9252200-9268800	Weak transcription	Primary T cells from cord blood	blood
33	chr12:9252600-9264800	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr12:9252600-9268400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr12:9252600-9268400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:9254200-9261200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:9254200-9264800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:9254200-9265800	Weak transcription	Gastric	stomach
39	chr12:9254200-9267600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:9254400-9261200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:9254800-9265800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr12:9255000-9261800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:9255200-9266000	Weak transcription	Fetal Stomach	stomach
44	chr12:9257000-9265800	Weak transcription	Brain Substantia Nigra	brain
45	chr12:9257600-9261200	Weak transcription	Ovary	ovary
46	chr12:9257800-9264800	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:9258200-9265400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:9258400-9267600	Weak transcription	Placenta	Placenta
49	chr12:9258800-9261400	Strong transcription	Aorta	Aorta
50	chr12:9258800-9262800	Strong transcription	Skeletal Muscle Male	skeletal muscle

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