Variant report

Variant	rs7039109
Chromosome Location	chr9:109716111-109716112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:109674332..109676607-chr9:109714900..109717890,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12003150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12005883	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12350828	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12684556	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12685671	0.94[ASN][1000 genomes]
rs12686587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1546484	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs16925955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16925965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs16926035	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs16926052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2417761	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs28633093	0.99[ASN][1000 genomes]
rs3764523	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs57147563	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57466834	0.97[ASN][1000 genomes]
rs58231792	0.94[ASN][1000 genomes]
rs58403995	0.98[ASN][1000 genomes]
rs58419285	0.94[ASN][1000 genomes]
rs58431218	1.00[ASN][1000 genomes]
rs58984661	0.98[ASN][1000 genomes]
rs60354530	0.94[ASN][1000 genomes]
rs60858521	0.94[ASN][1000 genomes]
rs6477551	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6477552	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7031901	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7043419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73524922	0.97[ASN][1000 genomes]
rs73524927	0.94[ASN][1000 genomes]
rs73524936	0.94[ASN][1000 genomes]
rs7847708	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs7848294	1.00[CEU][hapmap]
rs7848891	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7851411	1.00[CEU][hapmap]
rs7860806	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7865611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs7874076	1.00[CEU][hapmap]

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	nsv869202	chr9:108940763-109811530	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869351	chr9:109593212-110191170	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv831680	chr9:109653596-109848827	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7039109	S100A12	trans	brain	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:109686200-109722600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:109688600-109738600	Weak transcription	Primary hematopoietic stem cells	blood
3	chr9:109690400-109728600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr9:109692000-109734200	Weak transcription	Colonic Mucosa	Colon
5	chr9:109698000-109721400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr9:109698000-109721600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr9:109698000-109722400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:109699200-109719000	Weak transcription	Pancreas	Pancrea
9	chr9:109700800-109724000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr9:109701400-109729600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:109702000-109717400	Weak transcription	Dnd41	blood
12	chr9:109702200-109732400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:109702400-109720400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr9:109702400-109730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:109702400-109734200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr9:109702400-109734200	Weak transcription	Lung	lung
17	chr9:109702600-109718600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:109702600-109734200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:109703600-109731800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:109703600-109734200	Weak transcription	Esophagus	oesophagus
21	chr9:109703600-109734200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:109703800-109729800	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:109704600-109721000	Weak transcription	Right Atrium	heart
24	chr9:109704800-109717000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:109704800-109736400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:109705000-109716200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:109705200-109721400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:109706000-109722600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:109707600-109728600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:109707800-109716800	Strong transcription	Fetal Intestine Large	intestine
31	chr9:109707800-109723400	Strong transcription	Fetal Lung	lung
32	chr9:109708400-109730800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:109708600-109718800	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:109708800-109718800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:109709600-109721000	Weak transcription	HUVEC	blood vessel
36	chr9:109709800-109718600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr9:109710600-109716800	Weak transcription	NHEK	skin
38	chr9:109710600-109720200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:109710800-109732000	Weak transcription	Fetal Brain Male	brain
40	chr9:109712200-109718400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr9:109712200-109720600	Weak transcription	Brain Substantia Nigra	brain
42	chr9:109712400-109720400	Weak transcription	Brain Anterior Caudate	brain
43	chr9:109713000-109716800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:109713000-109718400	Weak transcription	Fetal Heart	heart
45	chr9:109713200-109728200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:109713600-109721600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr9:109713600-109721800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:109713800-109716400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr9:109713800-109716600	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr9:109713800-109718000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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