Variant report

Variant	rs1805684
Chromosome Location	chr12:9226250-9226251
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	chr12:9226173-9228148	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:9224778-9228061	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9224537-9226563	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:9226130-9226538	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9225166..9226787-chr12:9475945..9478723,2	MCF-7	breast:

Variant related genes	Relation type
A2M	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11831631	1.00[LWK][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11831793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11832509	1.00[AMR][1000 genomes]
rs11833184	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11833893	1.00[AMR][1000 genomes]
rs1805686	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1805694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026223	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026224	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026228	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026231	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35040316	1.00[AMR][1000 genomes]
rs57018529	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58097118	1.00[AMR][1000 genomes]
rs58565807	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60105910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60289110	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73240200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73240201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73241907	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73241991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73241999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73246318	1.00[AMR][1000 genomes]
rs73246327	1.00[AMR][1000 genomes]
rs73246334	1.00[AMR][1000 genomes]
rs73246337	1.00[AMR][1000 genomes]
rs73246344	1.00[AMR][1000 genomes]
rs73246352	1.00[AMR][1000 genomes]
rs73246383	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:9218000-9226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:9218200-9232200	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
6	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
7	chr12:9218400-9228600	Weak transcription	Brain Anterior Caudate	brain
8	chr12:9218400-9230800	Weak transcription	Brain Hippocampus Middle	brain
9	chr12:9218400-9231000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:9218400-9234400	Weak transcription	Right Atrium	heart
11	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
13	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr12:9218600-9229400	Weak transcription	Colonic Mucosa	Colon
15	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
18	chr12:9218800-9230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
21	chr12:9219000-9233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:9219200-9226400	Weak transcription	Pancreas	Pancrea
23	chr12:9219200-9229200	Weak transcription	Gastric	stomach
24	chr12:9219200-9234600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
26	chr12:9219400-9233200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:9219800-9233200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:9219800-9235800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:9220600-9232600	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:9220800-9227000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:9220800-9232400	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr12:9221000-9228600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:9222200-9230600	Genic enhancers	Liver	Liver
34	chr12:9222600-9232600	Strong transcription	Fetal Lung	lung
35	chr12:9222600-9233400	Strong transcription	Left Ventricle	heart
36	chr12:9223000-9227600	Strong transcription	Aorta	Aorta
37	chr12:9223000-9228000	Strong transcription	Spleen	Spleen
38	chr12:9223400-9226800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:9223800-9227600	Strong transcription	Duodenum Mucosa	Duodenum
40	chr12:9224000-9227000	Strong transcription	Colon Smooth Muscle	Colon
41	chr12:9224200-9227000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:9224200-9227200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:9224200-9232800	Strong transcription	Right Ventricle	heart
44	chr12:9224400-9227000	Weak transcription	Fetal Brain Male	brain
45	chr12:9224600-9226600	Enhancers	Fetal Intestine Large	intestine
46	chr12:9224600-9227000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr12:9224800-9227000	Strong transcription	Placenta	Placenta
48	chr12:9224800-9227200	Enhancers	Fetal Intestine Small	intestine
49	chr12:9225000-9227200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:9225000-9227400	Strong transcription	Fetal Stomach	stomach

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