Variant report

Variant	rs7018943
Chromosome Location	chr9:26869532-26869533
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	chr9:26867603..26870334-chr9:26891418..26893651,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120159	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1011358	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10511796	0.95[CHB][hapmap]
rs10812478	0.86[EUR][1000 genomes]
rs10812480	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10812485	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10812494	0.85[JPT][hapmap]
rs10812509	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs10812510	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10812517	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs10967541	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs10967550	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10967560	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10967565	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10967566	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10967575	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10967581	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];1.00[ASN][1000 genomes]
rs10967586	0.95[CHB][hapmap]
rs10967597	0.80[JPT][hapmap]
rs10967611	0.83[GIH][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap]
rs10967621	0.84[CHB][hapmap]
rs10967627	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10967630	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10967633	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs10967635	0.84[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap]
rs10967649	0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap]
rs10967650	0.84[CHB][hapmap]
rs10967661	0.81[CHD][hapmap]
rs10967678	0.84[CHB][hapmap]
rs10967681	0.84[CHB][hapmap]
rs10967688	0.84[CHB][hapmap]
rs12236850	0.84[CHD][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap]
rs12238317	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12345197	0.85[ASN][1000 genomes]
rs1336337	0.94[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs17760657	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17760820	0.95[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs17833941	0.84[JPT][hapmap]
rs2184739	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737226	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3739544	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs3739547	0.94[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.83[ASN][1000 genomes]
rs3739548	0.84[ASN][1000 genomes]
rs3739550	0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs4316229	0.96[ASN][1000 genomes]
rs7019034	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7019075	0.81[ASN][1000 genomes]
rs7033238	0.82[ASN][1000 genomes]
rs7035447	0.84[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.92[MEX][hapmap]
rs7857447	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs7857466	0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7869798	0.94[CHB][hapmap]
rs7871868	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7872666	0.83[ASN][1000 genomes]
rs7873073	0.90[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.84[ASN][1000 genomes]
rs7874940	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs7875171	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs9644870	0.84[CHB][hapmap];0.86[CHD][hapmap];0.92[MEX][hapmap]

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	nsv1026827	chr9:26693515-26904699	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7018943	IFT74	cis	Thyroid	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26822200-26889400	Weak transcription	Psoas Muscle	Psoas
2	chr9:26832200-26878400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:26834000-26882400	Weak transcription	HUVEC	blood vessel
4	chr9:26834200-26870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:26834200-26878400	Weak transcription	Brain Angular Gyrus	brain
6	chr9:26834200-26878600	Weak transcription	Spleen	Spleen
7	chr9:26834200-26880200	Weak transcription	Lung	lung
8	chr9:26834200-26880200	Weak transcription	NHEK	skin
9	chr9:26834200-26882200	Weak transcription	HMEC	breast
10	chr9:26834200-26888200	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr9:26834200-26891200	Weak transcription	NHDF-Ad	bronchial
12	chr9:26836400-26879600	Weak transcription	Esophagus	oesophagus
13	chr9:26836600-26891400	Weak transcription	Brain Substantia Nigra	brain
14	chr9:26838000-26878200	Weak transcription	Brain Germinal Matrix	brain
15	chr9:26838200-26879600	Weak transcription	Pancreas	Pancrea
16	chr9:26840600-26882400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:26840800-26879800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:26841200-26879800	Weak transcription	Colonic Mucosa	Colon
19	chr9:26842600-26882200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:26842800-26879600	Weak transcription	Thymus	Thymus
21	chr9:26843200-26878400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:26846400-26870600	Weak transcription	Fetal Stomach	stomach
23	chr9:26846600-26881600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr9:26847000-26883000	Weak transcription	K562	blood
25	chr9:26851400-26878600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:26851400-26888000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr9:26851800-26888600	Weak transcription	Fetal Heart	heart
28	chr9:26851800-26891600	Weak transcription	Stomach Mucosa	stomach
29	chr9:26852400-26888000	Weak transcription	NHLF	lung
30	chr9:26852800-26876000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:26853200-26878600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr9:26853600-26878200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr9:26853800-26870600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:26853800-26878400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr9:26853800-26878400	Weak transcription	Aorta	Aorta
36	chr9:26855000-26882200	Weak transcription	Right Ventricle	heart
37	chr9:26855400-26880200	Weak transcription	HepG2	liver
38	chr9:26855800-26888200	Weak transcription	NH-A	brain
39	chr9:26856000-26878800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:26856000-26881600	Weak transcription	Brain Hippocampus Middle	brain
41	chr9:26856000-26882200	Weak transcription	Brain Anterior Caudate	brain
42	chr9:26856000-26882200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:26856200-26878400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:26856200-26881400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:26856400-26878600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr9:26856600-26878600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:26856600-26888400	Weak transcription	Osteobl	bone
48	chr9:26857600-26891000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr9:26859400-26878200	Weak transcription	Ovary	ovary
50	chr9:26859400-26878400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links