Variant report

Variant	rs6668102
Chromosome Location	chr1:165631123-165631124
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	chr1:165631082..165632723-chr1:165632759..165634670,2	K562	blood:

Variant related genes	Relation type
ENSG00000143149	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10918234	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1577847	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348730	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426927	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6426928	0.91[ASW][hapmap];0.95[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.97[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426930	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667681	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681	1.00[CHD][hapmap]
rs6690818	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]
rs7355084	1.00[CHD][hapmap]
rs7511691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7516126	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533986	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534359	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553712	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333372	1.00[CHD][hapmap]
rs9333379	1.00[CHD][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6668102	NUF2	cis	cerebellum	SCAN
rs6668102	B4GALT3	cis	parietal	SCAN
rs6668102	MGST3	cis	parietal	SCAN
rs6668102	ALDH9A1	cis	cerebellum	SCAN
rs6668102	ALDH9A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165603800-165631200	Weak transcription	Fetal Kidney	kidney
2	chr1:165604800-165632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:165616400-165632000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:165617000-165631200	Strong transcription	Fetal Stomach	stomach
6	chr1:165618000-165638600	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:165618200-165652400	Strong transcription	Fetal Muscle Leg	muscle
8	chr1:165618600-165634800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:165618800-165638600	Strong transcription	Fetal Intestine Large	intestine
10	chr1:165619000-165635000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:165619000-165642600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:165619000-165643600	Strong transcription	Fetal Muscle Trunk	muscle
13	chr1:165619200-165634200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:165619200-165648800	Strong transcription	Liver	Liver
15	chr1:165619400-165636200	Strong transcription	Adipose Nuclei	Adipose
16	chr1:165619600-165642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:165619600-165653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:165620800-165631200	Weak transcription	HepG2	liver
19	chr1:165621000-165634400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:165621600-165632200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:165622800-165631200	Weak transcription	A549	lung
22	chr1:165623400-165653000	Weak transcription	Stomach Mucosa	stomach
23	chr1:165623800-165631200	Weak transcription	K562	blood
24	chr1:165623800-165631800	Weak transcription	HUVEC	blood vessel
25	chr1:165623800-165636400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:165624600-165632800	Weak transcription	Colonic Mucosa	Colon
27	chr1:165625000-165632200	Weak transcription	Brain Angular Gyrus	brain
28	chr1:165625600-165631800	Weak transcription	Fetal Brain Male	brain
29	chr1:165627200-165637400	Weak transcription	Right Ventricle	heart
30	chr1:165627400-165631200	Weak transcription	Fetal Heart	heart
31	chr1:165627400-165631600	Weak transcription	HMEC	breast
32	chr1:165627600-165632000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:165627600-165636600	Weak transcription	Psoas Muscle	Psoas
34	chr1:165628000-165633200	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:165628000-165634600	Strong transcription	Brain Hippocampus Middle	brain
36	chr1:165628000-165646600	Strong transcription	Primary T cells from cord blood	blood
37	chr1:165628600-165634400	Strong transcription	Lung	lung
38	chr1:165628600-165634400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:165628800-165631600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:165628800-165632200	Strong transcription	Left Ventricle	heart
41	chr1:165628800-165634400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:165628800-165634400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr1:165628800-165634600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr1:165628800-165639000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:165628800-165639000	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:165628800-165640200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:165628800-165642000	Strong transcription	HSMM	muscle
48	chr1:165628800-165642200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:165628800-165644000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:165628800-165646800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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