Variant report

Variant	rs12344865
Chromosome Location	chr9:97041555-97041556
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97021249..97023395-chr9:97039780..97042509,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175787	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10435925	0.96[AFR][1000 genomes]
rs10435926	0.96[ASN][1000 genomes]
rs10821327	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10993130	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10993137	0.84[ASN][1000 genomes]
rs10993140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10993144	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10993147	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11533012	0.91[AFR][1000 genomes]
rs11535539	0.88[AFR][1000 genomes]
rs12347577	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1328305	0.94[AFR][1000 genomes]
rs7027606	0.99[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7028040	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7045405	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9695761	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9696597	0.99[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831655	chr9:96834042-97042009	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	218 gene(s)	inside rSNPs	diseases
2	esv3394266	chr9:96935210-97045514	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS 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	195 gene(s)	inside rSNPs	diseases
3	nsv893592	chr9:96973995-97295269	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1046906	chr9:96999227-97239809	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv2761545	chr9:97025298-97356950	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 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	chr9:97022200-97041800	Weak transcription	Fetal Lung	lung
2	chr9:97022200-97042600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr9:97022200-97055200	Weak transcription	Aorta	Aorta
4	chr9:97022600-97055200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:97022800-97042400	Weak transcription	Brain Angular Gyrus	brain
6	chr9:97022800-97054600	Weak transcription	Pancreas	Pancrea
7	chr9:97023000-97041800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:97023000-97041800	Weak transcription	Esophagus	oesophagus
9	chr9:97023000-97050000	Weak transcription	Right Ventricle	heart
10	chr9:97023000-97055400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:97023400-97042800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:97029600-97041800	Weak transcription	Spleen	Spleen
13	chr9:97030200-97048400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr9:97030400-97042200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:97031800-97050400	Weak transcription	Psoas Muscle	Psoas
16	chr9:97032000-97041800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:97032400-97041600	Weak transcription	Fetal Intestine Small	intestine
18	chr9:97032400-97064600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:97032600-97041800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:97032800-97042200	Weak transcription	Fetal Kidney	kidney
21	chr9:97033600-97041800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr9:97033600-97054600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:97034000-97042400	Weak transcription	HMEC	breast
24	chr9:97034400-97041600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:97035400-97042000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr9:97035600-97042200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:97036800-97062600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:97037200-97042000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:97037400-97050200	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:97037600-97044600	Weak transcription	Fetal Stomach	stomach
31	chr9:97038800-97041600	Strong transcription	Primary B cells from cord blood	blood
32	chr9:97039200-97053600	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:97039200-97055000	Weak transcription	Brain Substantia Nigra	brain
34	chr9:97039200-97062600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr9:97039400-97054600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr9:97039400-97067600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:97039800-97042000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr9:97040000-97064600	Weak transcription	Brain Germinal Matrix	brain
39	chr9:97040200-97041800	Enhancers	Hela-S3	cervix
40	chr9:97040200-97042000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr9:97040400-97041600	Enhancers	HUVEC	blood vessel
42	chr9:97040400-97042000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr9:97040400-97042200	Enhancers	Placenta	Placenta
44	chr9:97040400-97043200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:97040400-97046000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr9:97040400-97046000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:97040400-97046000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
48	chr9:97040600-97041800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr9:97040600-97042000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr9:97040600-97043000	Strong transcription	Primary T helper naive cells from peripheral blood	blood

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