Variant report

Variant	rs6690818
Chromosome Location	chr1:165642867-165642868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165636460..165640030-chr1:165641604..165644830,4	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10918234	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1577847	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348730	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426927	1.00[ASN][1000 genomes]
rs6426928	0.95[CEU][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426930	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667681	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668102	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681	1.00[CHD][hapmap]
rs7355084	1.00[CHD][hapmap]
rs7511691	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533986	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534359	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544840	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551594	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553712	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554409	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333372	1.00[CHD][hapmap]
rs9333379	1.00[CHD][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	nsv946481	chr1:165639060-165646269	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6690818	ALDH9A1	cis	lymphoblastoid	seeQTL
rs6690818	MGST3	cis	parietal	SCAN
rs6690818	ALDH9A1	cis	cerebellum	SCAN
rs6690818	NUF2	cis	cerebellum	SCAN
rs6690818	B4GALT3	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165618200-165652400	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:165619000-165643600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:165619200-165648800	Strong transcription	Liver	Liver
5	chr1:165619600-165653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:165623400-165653000	Weak transcription	Stomach Mucosa	stomach
7	chr1:165628000-165646600	Strong transcription	Primary T cells from cord blood	blood
8	chr1:165628800-165644000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:165628800-165646800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:165628800-165646800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:165629000-165653600	Strong transcription	Dnd41	blood
12	chr1:165629200-165643600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:165629400-165652800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:165629400-165654200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:165629400-165656000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:165629600-165643000	Strong transcription	Primary B cells from cord blood	blood
17	chr1:165629600-165654800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr1:165629800-165643600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:165629800-165654800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:165630000-165654400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:165631000-165643400	Strong transcription	Hela-S3	cervix
22	chr1:165632200-165645400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:165632400-165649400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:165633600-165651200	Weak transcription	Pancreas	Pancrea
25	chr1:165633600-165651400	Weak transcription	Gastric	stomach
26	chr1:165633800-165651000	Weak transcription	Small Intestine	intestine
27	chr1:165634400-165644600	Weak transcription	Fetal Brain Male	brain
28	chr1:165634400-165651800	Weak transcription	Fetal Heart	heart
29	chr1:165634600-165644800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:165635200-165647800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:165635800-165645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:165635800-165648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:165636000-165652400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:165636400-165643600	Strong transcription	Fetal Intestine Small	intestine
35	chr1:165637800-165645400	Weak transcription	Right Ventricle	heart
36	chr1:165637800-165645400	Weak transcription	Spleen	Spleen
37	chr1:165637800-165645400	Weak transcription	HSMMtube	muscle
38	chr1:165637800-165648600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:165637800-165649200	Weak transcription	Aorta	Aorta
40	chr1:165637800-165651200	Weak transcription	NHEK	skin
41	chr1:165637800-165653400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr1:165638000-165645400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:165638000-165645400	Weak transcription	Lung	lung
44	chr1:165638000-165647800	Weak transcription	HMEC	breast
45	chr1:165638000-165666800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:165638200-165644600	Weak transcription	Brain Germinal Matrix	brain
47	chr1:165638200-165645400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:165638400-165645400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:165638400-165648000	Weak transcription	HepG2	liver
50	chr1:165638600-165644000	Weak transcription	Left Ventricle	heart

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