Variant report

Variant	rs9446085
Chromosome Location	chr6:69726362-69726363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1007921	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12194774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12194946	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12213405	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13191563	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs13192798	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13197569	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13205016	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs13205140	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs13219339	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1336634	1.00[JPT][hapmap]
rs1336635	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336636	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1336651	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1336655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1384246	1.00[JPT][hapmap]
rs1415029	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1415036	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];0.95[ASN][1000 genomes]
rs1482323	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs1556756	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16900400	1.00[CHB][hapmap]
rs1842743	1.00[JPT][hapmap]
rs1889877	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1889878	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2128290	1.00[JPT][hapmap]
rs2170508	1.00[JPT][hapmap]
rs2170509	1.00[JPT][hapmap]
rs2200088	1.00[JPT][hapmap]
rs2210867	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2225803	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2343396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2785576	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs2793459	1.00[JPT][hapmap]
rs35797298	0.86[ASN][1000 genomes]
rs3734465	1.00[JPT][hapmap]
rs3757046	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3757051	1.00[JPT][hapmap]
rs3798980	0.89[CHD][hapmap]
rs3798996	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[ASN][1000 genomes]
rs3798999	0.82[CEU][hapmap]
rs3799002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3799007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs3799016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799017	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3799021	0.89[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3799023	1.00[JPT][hapmap]
rs3799028	1.00[JPT][hapmap]
rs3799030	1.00[JPT][hapmap]
rs3799039	1.00[JPT][hapmap]
rs3823066	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3823067	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];0.95[ASN][1000 genomes]
rs4554293	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs524359	1.00[JPT][hapmap]
rs526898	0.85[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs557184	1.00[JPT][hapmap]
rs570181	1.00[JPT][hapmap]
rs602406	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs62416781	0.81[ASN][1000 genomes]
rs634371	0.85[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs634695	0.80[CEU][hapmap];1.00[JPT][hapmap]
rs635863	1.00[JPT][hapmap]
rs6455309	1.00[JPT][hapmap]
rs653895	1.00[JPT][hapmap]
rs6903686	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6904267	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6908180	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs6930865	1.00[JPT][hapmap]
rs6934473	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7739849	1.00[JPT][hapmap]
rs7741493	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7743332	0.94[ASW][hapmap];0.96[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];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756040	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756358	1.00[JPT][hapmap]
rs7756637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760307	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7761270	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs7764479	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7767118	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs779017	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs9342740	1.00[JPT][hapmap]
rs9346261	1.00[JPT][hapmap]
rs9360371	1.00[JPT][hapmap]
rs9360372	1.00[JPT][hapmap]
rs9454674	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9454695	1.00[JPT][hapmap]
rs947221	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs964664	1.00[JPT][hapmap]
rs994381	1.00[JPT][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	nsv886137	chr6:69684850-70095690	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9446085	MGC14436	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:69685800-69758800	Weak transcription	Fetal Brain Male	brain
2	chr6:69701000-69737600	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:69702400-69728600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:69702400-69737600	Weak transcription	Brain Angular Gyrus	brain
5	chr6:69720400-69758600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:69721400-69728600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:69721400-69728800	Weak transcription	Left Ventricle	heart
8	chr6:69721600-69752200	Weak transcription	Fetal Lung	lung
9	chr6:69723400-69742600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:69725000-69726400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:69725400-69727200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:69725600-69727000	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:69725800-69726600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr6:69725800-69727400	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr6:69726000-69726800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr6:69726200-69726600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:69726200-69727000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links