Variant report

Variant	rs4145028
Chromosome Location	chr6:74783557-74783558
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs2486227	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2486228	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132146	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4132147	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4145026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145027	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4345361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4374799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495244	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4640857	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4706567	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910804	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7745418	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755636	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9341448	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9360733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030389	chr6:74606701-74811706	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3394316	chr6:74630005-74935625	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv603733	chr6:74666559-74944460	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv3327625	chr6:74716120-74971605	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv3440413	chr6:74741688-74791357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv886161	chr6:74765488-74800529	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1017333	chr6:74776830-74907758	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv538307	chr6:74776830-74907758	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4145028	SEMA4D	trans	lymphoblastoid	seeQTL
rs4145028	C6orf150	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74782800-74783600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:74782800-74783600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:74782800-74783800	Enhancers	Fetal Intestine Small	intestine
4	chr6:74782800-74784200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:74782800-74784200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr6:74782800-74784200	Enhancers	NHLF	lung
7	chr6:74782800-74784400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:74782800-74784600	Enhancers	Fetal Muscle Leg	muscle
9	chr6:74782800-74784600	Enhancers	Fetal Stomach	stomach
10	chr6:74782800-74784800	Enhancers	Osteobl	bone
11	chr6:74782800-74785400	Enhancers	NHEK	skin
12	chr6:74782800-74785800	Enhancers	NHDF-Ad	bronchial
13	chr6:74782800-74786000	Enhancers	Colon Smooth Muscle	Colon
14	chr6:74782800-74786000	Enhancers	HMEC	breast
15	chr6:74782800-74786200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:74783000-74784200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:74783000-74785400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:74783000-74785600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:74783000-74786000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:74783200-74783600	Weak transcription	NH-A	brain
21	chr6:74783200-74784200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:74783200-74784600	Enhancers	Rectal Smooth Muscle	rectum
23	chr6:74783200-74784600	Enhancers	Stomach Smooth Muscle	stomach
24	chr6:74783400-74783600	Enhancers	HSMM	muscle

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