Variant report

Variant	rs41418445
Chromosome Location	chr1:67055798-67055799
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10128053	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11208911	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11208922	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs11208940	0.90[JPT][hapmap]
rs11208952	0.83[CEU][hapmap]
rs12062570	0.90[JPT][hapmap]
rs12069946	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12070270	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12072937	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12074963	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12085282	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12091471	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12091475	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12094526	0.90[JPT][hapmap]
rs13376692	0.93[CEU][hapmap]
rs1445573	0.94[ASW][hapmap];0.96[YRI][hapmap]
rs1530491	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs17129101	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs17129226	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs17129244	0.94[CEU][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs17129245	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs17129252	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs17129269	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs17129307	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs17440390	0.94[CEU][hapmap]
rs1832417	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs1867631	0.83[YRI][hapmap]
rs1988415	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs20354	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs2166307	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2182110	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs3901541	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs41405244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs41511845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4655642	0.81[JPT][hapmap]
rs5008753	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs6588210	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs6588211	0.94[CEU][hapmap];0.89[JPT][hapmap]
rs6588212	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs6588213	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs6664698	0.88[CEU][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap]
rs6670827	0.90[JPT][hapmap]
rs6690186	0.91[TSI][hapmap]
rs6694782	0.90[JPT][hapmap]
rs7520353	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7536634	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs7538967	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs7540244	0.94[CEU][hapmap];0.81[JPT][hapmap];0.91[TSI][hapmap]
rs7543378	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap]
rs7545674	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap]
rs920986	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs9787219	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013351	chr1:67039730-67055937	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv1003016	chr1:67043120-67067119	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1013476	chr1:67044630-67065911	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1221	chr1:67047908-67092696	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs41418445	TCTEX1D1	cis	parietal	SCAN
rs41418445	TCTEX1D1	cis	cerebellum	SCAN
rs41418445	SGIP1	cis	parietal	SCAN
rs41418445	ANGPTL3	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67041600-67062400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:67043200-67056800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:67043200-67064400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:67043400-67056200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:67043600-67066600	Weak transcription	Fetal Brain Male	brain
6	chr1:67044000-67057200	Weak transcription	Aorta	Aorta
7	chr1:67044200-67064000	Weak transcription	NH-A	brain
8	chr1:67044800-67064000	Weak transcription	Osteobl	bone
9	chr1:67045600-67056000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:67046400-67060400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:67049600-67062600	Weak transcription	Psoas Muscle	Psoas
12	chr1:67051000-67056200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:67051000-67060400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:67051000-67061600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:67051000-67064200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:67051000-67064400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:67051000-67065000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:67051200-67056200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:67051200-67056400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:67051200-67059000	Weak transcription	NHLF	lung
21	chr1:67051200-67063200	Weak transcription	NHDF-Ad	bronchial
22	chr1:67051200-67064200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:67051200-67064400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:67051200-67064400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:67051200-67066200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:67052200-67070800	Weak transcription	Fetal Heart	heart
27	chr1:67053800-67062200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:67055200-67055800	Enhancers	HepG2	liver
29	chr1:67055400-67064200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:67055400-67073000	Weak transcription	Left Ventricle	heart
31	chr1:67055600-67061400	Weak transcription	Fetal Brain Female	brain

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