Variant report

Variant	rs9450750
Chromosome Location	chr6:88296436-88296437
allele	C/T
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	chr6:88295798-88296525	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ORC3	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1052623	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs1075665	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11962148	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11965562	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs11970493	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11970696	0.90[CHB][hapmap]
rs12524205	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12529993	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12530371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13214442	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs16879887	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs16879893	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2223877	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs2246051	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2246057	0.90[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap]
rs2268996	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.80[TSI][hapmap]
rs2295088	0.95[CHB][hapmap];0.82[CHD][hapmap]
rs2300898	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2300899	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2300900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2300904	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs2300908	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs34513746	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3778671	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs3818057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4132446	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4354121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707378	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4707385	0.81[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs58305152	0.91[ASN][1000 genomes]
rs6454634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914244	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915077	0.90[CHB][hapmap]
rs6927171	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs6928057	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs728582	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs7649	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs7759462	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7761943	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9294384	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9294385	0.87[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9444499	0.90[CHB][hapmap]
rs9444501	0.90[CHB][hapmap]
rs9444509	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9444511	0.80[ASN][1000 genomes]
rs9444513	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9444514	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9444516	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444521	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444531	0.85[EUR][1000 genomes]
rs9444534	0.81[EUR][1000 genomes]
rs9450677	0.89[CHB][hapmap]
rs9450681	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9450686	0.90[CHB][hapmap]
rs9450693	0.90[CHB][hapmap]
rs9450694	0.83[CHB][hapmap]
rs9450697	0.89[CHB][hapmap]
rs9450698	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs9450699	1.00[CHB][hapmap]
rs9450700	1.00[CHB][hapmap]
rs9450708	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9450709	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs9450716	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450717	0.90[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs9450728	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450729	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9450734	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450735	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9450740	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9450741	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450743	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9450749	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9450751	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9450756	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9450760	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450763	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9474	0.94[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031961	chr6:88110401-88367006	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv538354	chr6:88273858-88311606	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9450750	C6orf162	cis	parietal	SCAN
rs9450750	AKIRIN2	cis	cerebellum	SCAN
rs9450750	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9450750	SLC35A1	cis	multi-tissue	Pritchard
rs9450750	SLC35A1	cis	parietal	SCAN
rs9450750	SLC35A1	cis	lymphoblastoid	seeQTL
rs9450750	C6orf162	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88227800-88298800	Weak transcription	Esophagus	oesophagus
2	chr6:88228400-88298400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:88256200-88297600	Weak transcription	Right Ventricle	heart
4	chr6:88272200-88297000	Weak transcription	Brain Germinal Matrix	brain
5	chr6:88272400-88297400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:88272400-88297400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:88273600-88298200	Weak transcription	Fetal Kidney	kidney
8	chr6:88274800-88298800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:88278800-88297400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:88283000-88296600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:88283000-88297000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:88283000-88298600	Weak transcription	Aorta	Aorta
13	chr6:88284400-88298000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:88284800-88298200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr6:88285200-88297400	Weak transcription	Brain Anterior Caudate	brain
16	chr6:88285400-88297200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr6:88285400-88297600	Weak transcription	Pancreas	Pancrea
18	chr6:88285600-88298200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:88286600-88297800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:88286800-88297800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:88289200-88297800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:88289200-88298600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:88289800-88298800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:88290000-88298000	Weak transcription	A549	lung
25	chr6:88290400-88298400	Weak transcription	Fetal Stomach	stomach
26	chr6:88290600-88297400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:88291000-88298000	Weak transcription	Thymus	Thymus
28	chr6:88291800-88298800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr6:88292400-88298200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr6:88292600-88296800	Weak transcription	Colon Smooth Muscle	Colon
31	chr6:88292600-88297400	Weak transcription	Fetal Lung	lung
32	chr6:88292600-88297600	Weak transcription	Lung	lung
33	chr6:88292600-88297600	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:88292600-88297800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr6:88292600-88297800	Weak transcription	HMEC	breast
36	chr6:88292600-88298000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:88292600-88298000	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:88292800-88297400	Weak transcription	NHEK	skin
39	chr6:88292800-88297600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:88292800-88297600	Weak transcription	NH-A	brain
41	chr6:88292800-88297800	Weak transcription	NHDF-Ad	bronchial
42	chr6:88292800-88298400	Weak transcription	HSMMtube	muscle
43	chr6:88293000-88297000	Enhancers	HepG2	liver
44	chr6:88293000-88297800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr6:88293000-88297800	Weak transcription	Osteobl	bone
46	chr6:88293000-88298000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr6:88293200-88297400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:88293200-88298000	Weak transcription	HSMM	muscle
49	chr6:88293200-88298200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr6:88293400-88297400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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