Variant report

Variant	rs56345025
Chromosome Location	chr12:9256219-9256220
allele	C/T
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	chr12:9255817-9257289	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9256071-9256511	HepG2	liver:	n/a	n/a
3	STAT3	chr12:9256159-9256316	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr12:9250026-9260702	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9255729-9257195	HepG2	liver:	n/a	n/a
6	CEBPB	chr12:9256004-9256238	A549	lung:	n/a	n/a
7	POLR2A	chr12:9256056-9257091	HepG2	liver:	n/a	n/a
8	MBD4	chr12:9253090-9260788	HepG2	liver:	n/a	n/a
9	POLR2A	chr12:9253697-9256933	HepG2	liver:	n/a	n/a
10	POLR2A	chr12:9252994-9260800	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1012588	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10492115	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11611433	0.88[ASN][1000 genomes]
rs11613746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615091	0.88[ASN][1000 genomes]
rs11615143	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615434	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16917971	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1805665	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1805680	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1863838	0.81[ASN][1000 genomes]
rs226406	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs226407	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3026229	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3741850	0.81[ASN][1000 genomes]
rs3741852	0.81[ASN][1000 genomes]
rs4882976	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882978	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4882979	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4883213	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56256934	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487609	0.96[ASN][1000 genomes]
rs6487636	0.81[ASN][1000 genomes]
rs7298673	0.81[ASN][1000 genomes]
rs7302725	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73048097	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73050004	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73050007	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73050013	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73051904	0.96[ASN][1000 genomes]
rs74061406	0.88[ASN][1000 genomes]
rs7955497	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7965529	0.81[ASN][1000 genomes]
rs7967997	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7970135	0.81[ASN][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:64 , 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	chr12:9236600-9258800	Weak transcription	Fetal Heart	heart
6	chr12:9237200-9261200	Strong transcription	Liver	Liver
7	chr12:9237200-9265200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:9237400-9264200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:9237800-9258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:9238600-9265800	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:9239400-9262800	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:9239400-9264000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:9239600-9265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:9240800-9267600	Weak transcription	Fetal Intestine Large	intestine
15	chr12:9241200-9262800	Strong transcription	Adipose Nuclei	Adipose
16	chr12:9241600-9264000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9243000-9274800	Weak transcription	Small Intestine	intestine
18	chr12:9243400-9265400	Weak transcription	Fetal Muscle Leg	muscle
19	chr12:9244200-9265200	Weak transcription	Brain Anterior Caudate	brain
20	chr12:9245000-9266000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:9245200-9259200	Weak transcription	Fetal Intestine Small	intestine
22	chr12:9245400-9256600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:9246200-9265200	Weak transcription	Fetal Brain Male	brain
24	chr12:9246600-9266000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:9246600-9268600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:9248000-9257200	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:9248000-9262600	Strong transcription	Left Ventricle	heart
28	chr12:9249400-9268800	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:9249600-9267600	Weak transcription	HSMMtube	muscle
30	chr12:9250000-9262800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr12:9250600-9268200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:9250600-9268600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:9251000-9266000	Weak transcription	NHLF	lung
34	chr12:9251200-9257200	Strong transcription	Right Ventricle	heart
35	chr12:9251200-9264800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:9251400-9268200	Weak transcription	Pancreas	Pancrea
37	chr12:9252200-9265200	Weak transcription	Colonic Mucosa	Colon
38	chr12:9252200-9268800	Weak transcription	Primary T cells from cord blood	blood
39	chr12:9252600-9256400	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:9252600-9259600	Weak transcription	Psoas Muscle	Psoas
41	chr12:9252600-9259800	Strong transcription	HepG2	liver
42	chr12:9252600-9264800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:9252600-9268400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:9252600-9268400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:9253000-9256600	Weak transcription	Fetal Lung	lung
46	chr12:9253400-9258400	Strong transcription	Placenta	Placenta
47	chr12:9254000-9258600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:9254200-9259600	Weak transcription	Spleen	Spleen
49	chr12:9254200-9261200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:9254200-9264800	Weak transcription	Duodenum Mucosa	Duodenum

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