Variant report

Variant	rs12346675
Chromosome Location	chr9:72957541-72957542
allele	C/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	chr9:72957353-72958482	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72956192..72958167-chr9:72961321..72962901,2	K562	blood:

Variant related genes	Relation type
SMC5	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10868798	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1104709	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11142141	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11142346	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11142355	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11793851	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1180085	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1180090	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1180093	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1180095	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1180109	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1180116	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1180131	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12338030	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12352944	0.81[EUR][1000 genomes]
rs12684881	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2183361	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4744593	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58704591	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62570318	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7019433	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7023586	0.83[EUR][1000 genomes]
rs7028657	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72712267	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72712271	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72712284	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847861	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849942	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7868421	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7873075	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription 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	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers 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 target site	19 gene(s)	inside rSNPs	diseases
3	nsv1049132	chr9:72895382-73005897	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72913800-72957800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:72926400-72965000	Weak transcription	Fetal Brain Male	brain
3	chr9:72926400-72967000	Weak transcription	Fetal Heart	heart
4	chr9:72936000-72970800	Weak transcription	Psoas Muscle	Psoas
5	chr9:72939600-72974000	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:72941200-72965000	Weak transcription	Hela-S3	cervix
7	chr9:72941400-72965200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr9:72942800-72961400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:72943000-72966400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr9:72943000-72966600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr9:72943200-72968600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:72943400-72963400	Weak transcription	HepG2	liver
13	chr9:72943400-72967200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:72943600-72970800	Weak transcription	Gastric	stomach
15	chr9:72944000-72957600	Weak transcription	Brain Anterior Caudate	brain
16	chr9:72944000-72962000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:72944000-72963200	Weak transcription	Pancreas	Pancrea
18	chr9:72944000-72963400	Weak transcription	Small Intestine	intestine
19	chr9:72944000-72963600	Weak transcription	Fetal Brain Female	brain
20	chr9:72944000-72965200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:72944000-72965200	Weak transcription	Colonic Mucosa	Colon
22	chr9:72944000-72970800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:72944000-72974600	Weak transcription	Aorta	Aorta
24	chr9:72944000-72978800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr9:72944000-73002600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:72944200-72961400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr9:72944200-72961600	Weak transcription	Brain Germinal Matrix	brain
28	chr9:72944200-72961800	Weak transcription	Brain Angular Gyrus	brain
29	chr9:72944200-72963200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:72944200-72963400	Weak transcription	Esophagus	oesophagus
31	chr9:72944200-72964600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr9:72944200-72968600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:72944200-72974000	Weak transcription	Spleen	Spleen
34	chr9:72944200-72974800	Weak transcription	Lung	lung
35	chr9:72944400-72959600	Weak transcription	NHLF	lung
36	chr9:72944400-72963200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr9:72944400-72963800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:72944400-72964000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr9:72944400-72965200	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:72944400-72965200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr9:72944400-72966000	Weak transcription	Right Ventricle	heart
42	chr9:72944600-72964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr9:72944800-72960800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:72945000-72960200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr9:72945000-72965000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr9:72945200-72963600	Weak transcription	Thymus	Thymus
47	chr9:72946800-72961600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:72947200-72961400	Weak transcription	Adipose Nuclei	Adipose
49	chr9:72947400-72960800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr9:72947400-72965400	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links