Variant report

Variant	rs11967399
Chromosome Location	chr6:119313517-119313518
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11967889	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526935	0.83[ASN][1000 genomes]
rs1413906	0.82[ASN][1000 genomes]
rs1539434	0.81[ASN][1000 genomes]
rs1570493	0.83[ASN][1000 genomes]
rs17513308	0.84[ASN][1000 genomes]
rs1762200	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2051056	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2051057	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295709	0.94[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs2357020	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2357030	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2782575	0.95[ASN][1000 genomes]
rs2797352	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs284919	0.94[CHB][hapmap]
rs2884078	0.88[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs4946383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4946384	0.80[ASN][1000 genomes]
rs4946388	0.82[ASN][1000 genomes]
rs4946389	0.82[ASN][1000 genomes]
rs4946390	0.82[ASN][1000 genomes]
rs57100274	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57285368	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910327	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6910850	0.82[CHB][hapmap]
rs6931558	0.81[ASN][1000 genomes]
rs6937499	0.81[ASN][1000 genomes]
rs7742473	0.88[JPT][hapmap]
rs7756475	0.82[ASN][1000 genomes]
rs7764418	0.84[ASN][1000 genomes]
rs794259	0.80[JPT][hapmap]
rs794260	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs794261	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794262	0.93[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794263	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794264	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794266	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs794614	1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs808028	0.82[ASN][1000 genomes]
rs813812	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9320673	0.81[ASN][1000 genomes]
rs9374757	0.81[ASN][1000 genomes]
rs9374777	0.88[CHB][hapmap];0.86[CHD][hapmap]
rs9387609	0.81[ASN][1000 genomes]
rs9387629	0.83[ASN][1000 genomes]
rs9387630	0.81[ASN][1000 genomes]
rs9398499	0.83[ASN][1000 genomes]
rs9401113	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9401118	0.88[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs9481881	0.82[ASN][1000 genomes]
rs9489526	0.88[JPT][hapmap]
rs9489543	0.81[JPT][hapmap]
rs954753	0.82[ASN][1000 genomes]
rs962393	0.82[CHB][hapmap];0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3340393	chr6:119311737-119316304	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
2	esv3442213	chr6:119311747-119316306	Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11967399	MCM9	cis	parietal	SCAN
rs11967399	C6orf204	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119285800-119340000	Weak transcription	Fetal Brain Male	brain
2	chr6:119287200-119326600	Weak transcription	Fetal Brain Female	brain
3	chr6:119287400-119330000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:119288800-119315000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:119292400-119344000	Weak transcription	Brain Germinal Matrix	brain
6	chr6:119293200-119345400	Weak transcription	Lung	lung
7	chr6:119294200-119330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:119296800-119314600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:119299600-119314600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:119300600-119344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr6:119300800-119319600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:119300800-119342600	Weak transcription	Brain Anterior Caudate	brain
13	chr6:119301000-119321800	Weak transcription	Placenta	Placenta
14	chr6:119301400-119319200	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:119311400-119314600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:119311400-119315800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:119313000-119329800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:119313200-119314200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:119313400-119314200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links