Variant report

Variant	rs6670673
Chromosome Location	chr1:56055190-56055191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1039294	0.84[CEU][hapmap]
rs10493193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10493195	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11206626	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206627	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11206635	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs11206649	0.85[CEU][hapmap]
rs1165460	1.00[CHB][hapmap]
rs11801001	0.92[CEU][hapmap]
rs11805740	0.92[CEU][hapmap];0.98[EUR][1000 genomes]
rs12059018	0.95[ASN][1000 genomes]
rs12071564	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap]
rs12081733	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12088041	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12116670	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12117758	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs12125730	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs12139482	1.00[CEU][hapmap]
rs17112410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17112413	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17418048	0.85[CEU][hapmap]
rs17418151	0.85[CEU][hapmap]
rs17452287	0.85[CEU][hapmap]
rs1846562	0.98[EUR][1000 genomes]
rs1846563	0.95[EUR][1000 genomes]
rs59236443	0.98[ASN][1000 genomes]
rs59539072	0.98[ASN][1000 genomes]
rs60149406	0.98[ASN][1000 genomes]
rs61566671	0.97[EUR][1000 genomes]
rs6588567	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6677373	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6680818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681925	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6694680	0.98[EUR][1000 genomes]
rs6694786	0.92[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7519540	0.85[CEU][hapmap]
rs7520444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7548272	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7549716	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7550575	0.85[CEU][hapmap]
rs769970	0.97[EUR][1000 genomes]
rs769989	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]

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	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv461617	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv546303	chr1:56055190-56123510	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6670673	ZYG11A	cis	parietal	SCAN
rs6670673	GLIS1	cis	cerebellum	SCAN
rs6670673	CPT2	cis	cerebellum	SCAN
rs6670673	DAB1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:56050600-56055400	Weak transcription	Ovary	ovary
3	chr1:56050800-56057800	Weak transcription	Right Ventricle	heart
4	chr1:56051000-56055200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr1:56051000-56055200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:56051000-56055800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:56051200-56055200	Weak transcription	Adipose Nuclei	Adipose
8	chr1:56051200-56055200	Weak transcription	HSMM	muscle
9	chr1:56051200-56055400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:56051200-56057200	Weak transcription	Fetal Heart	heart
11	chr1:56051400-56055400	Weak transcription	NHLF	lung
12	chr1:56052600-56057800	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:56052800-56055400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:56052800-56055400	Weak transcription	Left Ventricle	heart
15	chr1:56052800-56055400	Weak transcription	Psoas Muscle	Psoas
16	chr1:56052800-56055400	Weak transcription	Right Atrium	heart
17	chr1:56052800-56060400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:56053800-56056000	Enhancers	Fetal Stomach	stomach
19	chr1:56053800-56058400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:56053800-56058400	Enhancers	NHDF-Ad	bronchial
21	chr1:56054000-56055200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:56054000-56055800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr1:56054400-56055200	Enhancers	Osteobl	bone
24	chr1:56054400-56055600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:56054400-56059000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr1:56054600-56055400	Weak transcription	Fetal Lung	lung
27	chr1:56054600-56058000	Weak transcription	Aorta	Aorta
28	chr1:56055000-56055400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:56055000-56056200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:56055000-56056200	Enhancers	Fetal Muscle Leg	muscle
31	chr1:56055000-56056200	Enhancers	HMEC	breast

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