Variant report

Variant	rs428406
Chromosome Location	chr6:75902950-75902951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:75902409-75903279	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:75900606..75903271-chr6:75905773..75909365,3	K562	blood:

Variant related genes	Relation type
COL12A1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11961252	0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs1203221	1.00[AMR][1000 genomes]
rs171262	1.00[AMR][1000 genomes]
rs171266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs173279	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs181179	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240361	1.00[YRI][hapmap]
rs240362	1.00[YRI][hapmap]
rs240364	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240372	1.00[AMR][1000 genomes]
rs240373	1.00[AMR][1000 genomes]
rs240391	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs240407	1.00[AMR][1000 genomes]
rs240434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240436	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240716	0.91[YRI][hapmap]
rs240718	0.84[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs240739	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs240740	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs240742	0.84[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2703709	1.00[AMR][1000 genomes]
rs2808192	1.00[AMR][1000 genomes]
rs2842449	1.00[AMR][1000 genomes]
rs2842454	1.00[AMR][1000 genomes]
rs2842460	1.00[AMR][1000 genomes]
rs2951941	1.00[AMR][1000 genomes]
rs2998372	1.00[AMR][1000 genomes]
rs2998373	1.00[AMR][1000 genomes]
rs2998375	1.00[AMR][1000 genomes]
rs2998378	1.00[AMR][1000 genomes]
rs34807169	1.00[AMR][1000 genomes]
rs471960	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs480888	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55862072	1.00[AMR][1000 genomes]
rs578715	0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58299431	1.00[AMR][1000 genomes]
rs58347254	1.00[AMR][1000 genomes]
rs588100	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs598034	0.82[YRI][hapmap]
rs601008	0.80[AFR][1000 genomes]
rs612266	0.91[YRI][hapmap]
rs683406	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73751107	1.00[AMR][1000 genomes]
rs73751108	1.00[AMR][1000 genomes]
rs73751109	1.00[AMR][1000 genomes]
rs73751816	1.00[AMR][1000 genomes]
rs73751817	1.00[AMR][1000 genomes]
rs73751820	1.00[AMR][1000 genomes]
rs73751824	1.00[AMR][1000 genomes]
rs73751826	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022377	chr6:75762463-75919592	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv538309	chr6:75762463-75919592	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv830697	chr6:75763095-75915029	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
8	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv886181	chr6:75852488-75919484	Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
11	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75877600-75905800	Strong transcription	HSMM	muscle
2	chr6:75887600-75911000	Weak transcription	Fetal Stomach	stomach
3	chr6:75891800-75906600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:75893800-75904800	Weak transcription	Left Ventricle	heart
5	chr6:75893800-75905600	Weak transcription	Hela-S3	cervix
6	chr6:75894600-75903000	Strong transcription	NHLF	lung
7	chr6:75894600-75906200	Strong transcription	Osteobl	bone
8	chr6:75896000-75903000	Strong transcription	NHDF-Ad	bronchial
9	chr6:75896800-75903800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:75896800-75907600	Weak transcription	Fetal Kidney	kidney
11	chr6:75897200-75904000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:75898200-75905000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr6:75898200-75906400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:75898400-75911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:75898400-75911600	Weak transcription	Aorta	Aorta
16	chr6:75898400-75911800	Weak transcription	HSMMtube	muscle
17	chr6:75898600-75906400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:75898600-75909800	Weak transcription	Fetal Muscle Leg	muscle
19	chr6:75898800-75904000	Weak transcription	NHEK	skin
20	chr6:75899000-75905000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:75899000-75908400	Weak transcription	Ovary	ovary
22	chr6:75899400-75904600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:75899400-75907000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:75899600-75904000	Weak transcription	Adipose Nuclei	Adipose
25	chr6:75899600-75909200	Weak transcription	Fetal Intestine Large	intestine
26	chr6:75899800-75911000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr6:75901000-75911600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr6:75901200-75910200	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:75901800-75908400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:75902000-75905400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:75902400-75904200	Strong transcription	NH-A	brain
32	chr6:75902400-75904400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:75902400-75904600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr6:75902600-75903200	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr6:75902600-75905800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:75902800-75903000	Strong transcription	HMEC	breast

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