Variant report

Variant	rs1410838
Chromosome Location	chr9:108146859-108146860
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	chr9:108146858-108147011	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SLC44A1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10991625	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991630	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991632	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991633	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991634	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991636	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10991638	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10991640	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10991641	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10991643	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10991644	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10991645	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11096	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12377753	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12377755	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12379026	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12379533	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12380580	1.00[CEU][hapmap];1.00[AMR][1000 genomes]
rs1360087	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs17246769	0.86[EUR][1000 genomes]
rs1969981	0.90[EUR][1000 genomes]
rs2149591	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2417641	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2771032	0.90[EUR][1000 genomes]
rs2771034	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2771043	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2812313	0.97[EUR][1000 genomes]
rs2812317	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs73514068	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
4	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
5	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:108097600-108147000	Weak transcription	HMEC	breast
7	chr9:108100200-108149600	Weak transcription	Pancreas	Pancrea
8	chr9:108104800-108147600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:108105000-108149600	Weak transcription	Right Ventricle	heart
10	chr9:108105000-108151200	Weak transcription	Gastric	stomach
11	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
12	chr9:108105200-108149800	Weak transcription	NHDF-Ad	bronchial
13	chr9:108117400-108147400	Weak transcription	Spleen	Spleen
14	chr9:108118200-108147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr9:108118600-108147600	Weak transcription	Primary B cells from peripheral blood	blood
16	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:108121800-108148600	Weak transcription	A549	lung
18	chr9:108122400-108148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:108122600-108153400	Weak transcription	Stomach Mucosa	stomach
20	chr9:108123600-108154400	Weak transcription	Colonic Mucosa	Colon
21	chr9:108123800-108147600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr9:108124200-108147000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr9:108124200-108147600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr9:108124400-108147400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:108124400-108151000	Weak transcription	Fetal Brain Male	brain
26	chr9:108124600-108151800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:108125200-108147000	Weak transcription	GM12878-XiMat	blood
29	chr9:108125400-108147000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:108125400-108147600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr9:108125400-108149800	Weak transcription	HSMMtube	muscle
32	chr9:108125600-108157000	Weak transcription	Osteobl	bone
33	chr9:108126000-108152000	Weak transcription	Brain Germinal Matrix	brain
34	chr9:108126400-108147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr9:108127000-108147800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr9:108127200-108151800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr9:108128200-108151400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:108130200-108147800	Weak transcription	Ovary	ovary
39	chr9:108130800-108147600	Weak transcription	Primary B cells from cord blood	blood
40	chr9:108132400-108147000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:108135000-108147600	Weak transcription	Thymus	Thymus
42	chr9:108136200-108152000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:108136400-108147000	Weak transcription	NHEK	skin
44	chr9:108137000-108147400	Weak transcription	Primary T cells from cord blood	blood
45	chr9:108137400-108150600	Weak transcription	Fetal Heart	heart
46	chr9:108137800-108147000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr9:108137800-108147200	Weak transcription	Colon Smooth Muscle	Colon
48	chr9:108137800-108147600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:108137800-108147600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr9:108137800-108147600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links