Variant report

Variant	rs171417
Chromosome Location	chr9:97945796-97945797
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	chr9:97941582..97943855-chr9:97944077..97946708,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

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	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[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];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs187172	1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[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];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[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];0.89[AMR][1000 genomes]
rs356673	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]
rs356675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[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];0.87[AMR][1000 genomes];0.96[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];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356679	0.89[AMR][1000 genomes];0.86[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];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs356682	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356683	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356687	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs356688	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[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];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[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];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437511	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[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	0.94[AMR][1000 genomes];0.94[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];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[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];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs609324	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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];0.96[AMR][1000 genomes];0.97[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];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs171417	NINJ1	cis	cerebellum	SCAN
rs171417	SYK	cis	parietal	SCAN
rs171417	PHF2	cis	cerebellum	SCAN
rs171417	TDRD7	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97906600-97950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr9:97920000-97952000	Weak transcription	Aorta	Aorta
3	chr9:97920000-97952000	Weak transcription	Esophagus	oesophagus
4	chr9:97920400-97951800	Weak transcription	HepG2	liver
5	chr9:97927600-97950400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97930600-97950400	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr9:97930600-97950800	Weak transcription	Thymus	Thymus
8	chr9:97930600-97952000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:97930800-97951600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:97930800-97952400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:97933200-97950600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:97939600-97950200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:97940200-97950200	Weak transcription	Fetal Lung	lung
14	chr9:97940600-97950600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr9:97940800-97950400	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:97941000-97952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:97941000-97959800	Weak transcription	Pancreas	Pancrea
18	chr9:97941800-97950400	Weak transcription	Gastric	stomach
19	chr9:97944200-97945800	Strong transcription	Fetal Intestine Small	intestine
20	chr9:97944400-97950600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:97944800-97945800	Strong transcription	Primary T cells from cord blood	blood
22	chr9:97944800-97946200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr9:97945000-97945800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:97945000-97946000	Enhancers	Fetal Heart	heart
25	chr9:97945000-97946000	Strong transcription	Fetal Intestine Large	intestine
26	chr9:97945000-97947000	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr9:97945200-97945800	Enhancers	Ovary	ovary
28	chr9:97945200-97946000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:97945200-97946200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:97945200-97946200	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr9:97945200-97946200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr9:97945200-97946200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:97945200-97946200	Enhancers	Brain Hippocampus Middle	brain
34	chr9:97945200-97946400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr9:97945200-97946400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr9:97945400-97945800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr9:97945400-97945800	Enhancers	Fetal Kidney	kidney
38	chr9:97945400-97945800	Enhancers	Right Ventricle	heart
39	chr9:97945400-97946000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:97945400-97946000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:97945400-97946000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr9:97945400-97946000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr9:97945400-97946000	Enhancers	Rectal Smooth Muscle	rectum
44	chr9:97945400-97946200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr9:97945400-97946200	Enhancers	H9 Cell Line	embryonic stem cell
46	chr9:97945400-97946200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr9:97945400-97946400	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr9:97945400-97948400	Weak transcription	Lung	lung
49	chr9:97945600-97945800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr9:97945600-97945800	Genic enhancers	Fetal Stomach	stomach

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