Variant report

Variant	rs226407
Chromosome Location	chr12:9245779-9245780
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	chr12:9242469-9248398	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9242414-9246918	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9244257-9246813	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9244325-9246829	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9242503-9246785	HepG2	liver:	n/a	n/a
6	MBD4	chr12:9244451-9246321	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:9245757-9245885	HepG2	liver:	n/a	n/a
8	MBD4	chr12:9245371-9245896	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1012588	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10492114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10492115	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11608867	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11609582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11613746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11615091	0.88[ASN][1000 genomes]
rs11615143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11615434	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11615443	1.00[JPT][hapmap]
rs16917971	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16918162	1.00[JPT][hapmap]
rs1805665	1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1805680	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863838	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs226406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3026229	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3213832	1.00[JPT][hapmap]
rs3741849	1.00[JPT][hapmap]
rs3741850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3741852	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4882976	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4882978	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4882979	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4883213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56256934	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56345025	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6487609	0.96[ASN][1000 genomes]
rs6487636	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6487650	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7298673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7302725	0.92[ASN][1000 genomes]
rs73048097	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73050004	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73050007	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73050013	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73051904	0.96[ASN][1000 genomes]
rs74061406	0.88[ASN][1000 genomes]
rs7955497	1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965529	0.81[ASN][1000 genomes]
rs7967997	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970135	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9888309	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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

No data

Chromatin state (count:51 , 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	chr12:9235000-9253600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:9235200-9265800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:9236600-9258800	Weak transcription	Fetal Heart	heart
7	chr12:9237200-9252200	Weak transcription	Psoas Muscle	Psoas
8	chr12:9237200-9261200	Strong transcription	Liver	Liver
9	chr12:9237200-9265200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:9237400-9264200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:9237600-9246000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:9237800-9258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:9238600-9246800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:9238600-9265800	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:9238800-9246600	Strong transcription	Stomach Smooth Muscle	stomach
16	chr12:9239400-9262800	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:9239400-9264000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:9239600-9265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:9240800-9267600	Weak transcription	Fetal Intestine Large	intestine
20	chr12:9241000-9246600	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr12:9241200-9246000	Strong transcription	Left Ventricle	heart
22	chr12:9241200-9247000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:9241200-9262800	Strong transcription	Adipose Nuclei	Adipose
24	chr12:9241600-9264000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:9242400-9246800	Strong transcription	Aorta	Aorta
26	chr12:9242400-9247000	Strong transcription	Ovary	ovary
27	chr12:9242600-9246200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr12:9242800-9246000	Strong transcription	Placenta	Placenta
29	chr12:9242800-9246800	Strong transcription	Fetal Stomach	stomach
30	chr12:9242800-9246800	Strong transcription	Spleen	Spleen
31	chr12:9243000-9246800	Strong transcription	Lung	lung
32	chr12:9243000-9251400	Weak transcription	Primary T cells from cord blood	blood
33	chr12:9243000-9274800	Weak transcription	Small Intestine	intestine
34	chr12:9243400-9265400	Weak transcription	Fetal Muscle Leg	muscle
35	chr12:9243600-9247000	Strong transcription	Fetal Lung	lung
36	chr12:9243800-9252000	Strong transcription	HepG2	liver
37	chr12:9244200-9265200	Weak transcription	Brain Anterior Caudate	brain
38	chr12:9244400-9246200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr12:9244600-9248400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:9244800-9245800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:9245000-9251200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:9245000-9266000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:9245200-9246800	Strong transcription	Right Ventricle	heart
44	chr12:9245200-9251800	Weak transcription	Colonic Mucosa	Colon
45	chr12:9245200-9254000	Weak transcription	Gastric	stomach
46	chr12:9245200-9259200	Weak transcription	Fetal Intestine Small	intestine
47	chr12:9245400-9245800	Genic enhancers	Colon Smooth Muscle	Colon
48	chr12:9245400-9256600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr12:9245600-9246200	Strong transcription	Fetal Brain Male	brain
50	chr12:9245600-9248800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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