Variant report

Variant	rs10499090
Chromosome Location	chr6:119321551-119321552
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	chr6:119319940..119322469-chr6:119324553..119327875,4	K562	blood:

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1022706	0.81[ASN][1000 genomes]
rs1022707	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1022708	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1022709	0.81[ASN][1000 genomes]
rs11153782	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs11965951	0.82[ASN][1000 genomes]
rs11967231	0.82[ASN][1000 genomes]
rs11967232	0.82[ASN][1000 genomes]
rs12527291	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12527363	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12664251	0.84[ASN][1000 genomes]
rs1807979	0.82[ASN][1000 genomes]
rs1885125	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2051057	0.80[JPT][hapmap]
rs2145569	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2145570	0.82[ASN][1000 genomes]
rs2180860	0.82[ASN][1000 genomes]
rs35906538	0.84[ASN][1000 genomes]
rs3756940	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3945959	0.82[ASN][1000 genomes]
rs4245502	0.82[ASN][1000 genomes]
rs4946369	0.82[ASN][1000 genomes]
rs4946370	0.82[ASN][1000 genomes]
rs4946371	0.81[ASN][1000 genomes]
rs4946372	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4946373	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4946374	0.82[ASN][1000 genomes]
rs4946376	0.82[ASN][1000 genomes]
rs4946377	0.82[ASN][1000 genomes]
rs4946378	0.82[ASN][1000 genomes]
rs4946380	0.85[ASN][1000 genomes]
rs4946382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4946385	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946386	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4946387	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55978448	0.84[ASN][1000 genomes]
rs62422265	0.82[ASN][1000 genomes]
rs62422266	0.81[ASN][1000 genomes]
rs62422267	0.82[ASN][1000 genomes]
rs62422268	0.82[ASN][1000 genomes]
rs62422270	0.81[ASN][1000 genomes]
rs6569035	0.84[ASN][1000 genomes]
rs6901738	0.84[ASN][1000 genomes]
rs6903220	0.84[ASN][1000 genomes]
rs6903579	0.82[ASN][1000 genomes]
rs6904381	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6910377	0.82[ASN][1000 genomes]
rs6916672	0.84[ASN][1000 genomes]
rs6918569	0.81[ASN][1000 genomes]
rs6918844	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6919100	0.81[ASN][1000 genomes]
rs6923637	0.84[ASN][1000 genomes]
rs6923771	0.82[ASN][1000 genomes]
rs6928315	0.82[ASN][1000 genomes]
rs6928945	0.82[ASN][1000 genomes]
rs6929403	0.90[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.83[ASN][1000 genomes]
rs6931074	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6933970	0.82[ASN][1000 genomes]
rs6935960	0.82[ASN][1000 genomes]
rs6939937	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6940120	0.84[ASN][1000 genomes]
rs72970476	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7381533	0.81[ASN][1000 genomes]
rs7381535	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7381546	0.82[ASN][1000 genomes]
rs7741149	0.82[ASN][1000 genomes]
rs7758729	0.84[ASN][1000 genomes]
rs7758849	0.83[ASN][1000 genomes]
rs7758862	0.83[ASN][1000 genomes]
rs7759423	0.82[ASN][1000 genomes]
rs9320669	0.82[ASN][1000 genomes]
rs9320670	0.82[ASN][1000 genomes]
rs9320671	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9374759	0.81[ASN][1000 genomes]
rs9374763	0.81[ASN][1000 genomes]
rs9374764	0.81[ASN][1000 genomes]
rs9374766	0.85[ASN][1000 genomes]
rs9374767	0.85[ASN][1000 genomes]
rs9385060	0.84[ASN][1000 genomes]
rs9385063	0.85[ASN][1000 genomes]
rs9387610	0.82[ASN][1000 genomes]
rs9387611	0.80[ASN][1000 genomes]
rs9387612	0.82[ASN][1000 genomes]
rs9387613	0.84[ASN][1000 genomes]
rs9387621	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9387624	0.90[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs9387626	0.84[ASN][1000 genomes]
rs9387628	0.81[ASN][1000 genomes]
rs9401103	0.85[ASN][1000 genomes]
rs9401106	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9489563	0.84[ASN][1000 genomes]
rs9489569	0.84[ASN][1000 genomes]
rs9689589	0.82[ASN][1000 genomes]
rs988098	0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs9968863	0.85[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	nsv1030400	chr6:119320153-119433830	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10499090	MCM9	cis	parietal	SCAN
rs10499090	C6orf204	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 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	chr6:119292400-119344000	Weak transcription	Brain Germinal Matrix	brain
5	chr6:119293200-119345400	Weak transcription	Lung	lung
6	chr6:119294200-119330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:119300600-119344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:119300800-119342600	Weak transcription	Brain Anterior Caudate	brain
9	chr6:119301000-119321800	Weak transcription	Placenta	Placenta
10	chr6:119313000-119329800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:119314400-119364400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:119315200-119325200	Weak transcription	Pancreas	Pancrea
13	chr6:119315400-119329800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:119315400-119330800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:119316600-119328800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:119318600-119344200	Weak transcription	Fetal Lung	lung
17	chr6:119319400-119330200	Weak transcription	Ovary	ovary
18	chr6:119319600-119321800	Enhancers	Fetal Intestine Large	intestine
19	chr6:119319600-119333600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:119319800-119342600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:119320000-119327000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr6:119320200-119321800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:119320400-119329200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:119321000-119323000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:119321400-119323000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:119321400-119325600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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