Variant report

Variant	rs6662330
Chromosome Location	chr1:67018728-67018729
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10789207	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10789208	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12083791	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12093875	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12144047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1338197	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17129012	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1856317	0.92[JPT][hapmap]
rs2068381	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2312151	0.95[CEU][hapmap];0.87[CHB][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4655617	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6690186	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs72677052	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7516148	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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	nsv1210	chr1:67017295-67033203	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6662330	TCTEX1D1	cis	parietal	SCAN
rs6662330	TCTEX1D1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67000400-67022000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:67000800-67029800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:67001200-67022000	Weak transcription	Right Ventricle	heart
4	chr1:67007000-67021800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:67009000-67019600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr1:67009600-67019600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:67009800-67028200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:67010000-67029000	Weak transcription	Fetal Kidney	kidney
9	chr1:67011000-67028000	Weak transcription	HUVEC	blood vessel
10	chr1:67011200-67021800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:67011200-67022000	Weak transcription	Pancreas	Pancrea
12	chr1:67011800-67029800	Weak transcription	Fetal Brain Male	brain
13	chr1:67012400-67021400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:67013800-67021200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:67015800-67021600	Weak transcription	Brain Anterior Caudate	brain
16	chr1:67017400-67023800	Enhancers	Fetal Heart	heart
17	chr1:67017600-67019000	Enhancers	Adipose Nuclei	Adipose
18	chr1:67017600-67019800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:67017600-67020200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:67017800-67018800	Enhancers	Left Ventricle	heart
21	chr1:67017800-67019000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:67017800-67019000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:67017800-67019000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:67017800-67019200	Enhancers	Fetal Thymus	thymus
25	chr1:67017800-67022400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:67018000-67018800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr1:67018000-67018800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:67018000-67018800	Enhancers	Fetal Muscle Leg	muscle
29	chr1:67018000-67018800	Enhancers	Gastric	stomach
30	chr1:67018000-67018800	Enhancers	Lung	lung
31	chr1:67018000-67019000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:67018000-67019000	Enhancers	Primary T cells from cord blood	blood
33	chr1:67018000-67019200	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:67018000-67019200	Enhancers	Brain Substantia Nigra	brain
35	chr1:67018000-67019200	Enhancers	Fetal Lung	lung
36	chr1:67018000-67020200	Enhancers	NHLF	lung
37	chr1:67018000-67023800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:67018200-67018800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr1:67018200-67018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:67018200-67018800	Enhancers	Aorta	Aorta
41	chr1:67018200-67019000	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr1:67018200-67019000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:67018200-67023800	Enhancers	Brain Angular Gyrus	brain
44	chr1:67018400-67019000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr1:67018400-67021400	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:67018400-67022000	Weak transcription	NH-A	brain
47	chr1:67018600-67019000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:67018600-67019000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr1:67018600-67019000	Enhancers	Brain Cingulate Gyrus	brain
50	chr1:67018600-67019000	Enhancers	Duodenum Smooth Muscle	Duodenum

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