Variant report

Variant	rs356673
Chromosome Location	chr9:97952655-97952656
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:97906541..97908120-chr9:97951638..97953781,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1045276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10491560	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs10761381	0.83[CHB][hapmap]
rs10821450	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs171417	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184818	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs187172	1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs2282216	0.85[JPT][hapmap]
rs356666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs356669	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes]
rs356675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356678	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356679	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs356680	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs356682	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356687	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs356688	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780567	0.90[JPT][hapmap]
rs3824486	0.85[JPT][hapmap]
rs416792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437511	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647376	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4647534	0.90[JPT][hapmap]
rs4744451	0.90[JPT][hapmap]
rs526189	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs540412	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs565293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs609324	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs657637	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7033633	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap]
rs944934	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs356673	TDRD7	cis	cerebellum	SCAN
rs356673	NINJ1	cis	cerebellum	SCAN
rs356673	PHF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97941000-97959800	Weak transcription	Pancreas	Pancrea
2	chr9:97945800-97952800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:97946200-97955600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:97946200-97955800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:97948800-97955600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:97948800-97955600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:97950400-97953000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:97950600-97952800	Enhancers	Primary T cells from cord blood	blood
9	chr9:97950600-97953400	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr9:97950800-97952800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:97950800-97959600	Weak transcription	Gastric	stomach
12	chr9:97951000-97952800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:97951400-97952800	Enhancers	Brain Germinal Matrix	brain
14	chr9:97951400-97953000	Enhancers	Right Ventricle	heart
15	chr9:97951600-97952800	Enhancers	Colon Smooth Muscle	Colon
16	chr9:97951600-97953200	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:97951800-97953000	Enhancers	Right Atrium	heart
18	chr9:97951800-97953000	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr9:97951800-97955000	Weak transcription	Thymus	Thymus
20	chr9:97952000-97952800	Enhancers	Primary hematopoietic stem cells	blood
21	chr9:97952000-97952800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr9:97952000-97952800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:97952000-97952800	Weak transcription	Fetal Brain Female	brain
24	chr9:97952000-97953000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:97952000-97953000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:97952000-97953000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:97952000-97953000	Enhancers	Esophagus	oesophagus
28	chr9:97952000-97953000	Enhancers	Left Ventricle	heart
29	chr9:97952000-97953000	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr9:97952000-97953200	Enhancers	Aorta	Aorta
31	chr9:97952000-97953200	Enhancers	Ovary	ovary
32	chr9:97952000-97953200	Enhancers	NHEK	skin
33	chr9:97952000-97953600	Enhancers	Lung	lung
34	chr9:97952200-97952800	Enhancers	Fetal Lung	lung
35	chr9:97952200-97953000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:97952200-97953000	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr9:97952200-97953000	Enhancers	Fetal Stomach	stomach
38	chr9:97952200-97953200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr9:97952200-97955600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:97952200-97960200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr9:97952400-97953000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr9:97952400-97953000	Enhancers	Fetal Muscle Trunk	muscle
43	chr9:97952400-97953000	Enhancers	HMEC	breast
44	chr9:97952400-97953000	Enhancers	HUVEC	blood vessel
45	chr9:97952400-97953200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr9:97952400-97955400	Weak transcription	GM12878-XiMat	blood
47	chr9:97952600-97952800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:97952600-97953800	Enhancers	Stomach Smooth Muscle	stomach
49	chr9:97952600-97963200	Weak transcription	Spleen	Spleen
50	chr9:97952600-97969400	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links