Variant report

Variant	rs240369
Chromosome Location	chr6:75919484-75919485
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	CTCF	chr6:75919400-75919690	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr6:75919400-75919550	NHLF	lung:	n/a	n/a
3	CTCF	chr6:75919380-75919530	AG10803	skin:	n/a	n/a
4	CTCF	chr6:75919380-75919530	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
COL12A1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs117512	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1203213	0.92[EUR][1000 genomes]
rs147523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs240361	1.00[JPT][hapmap]
rs240367	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs240368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240382	0.85[CEU][hapmap]
rs240385	0.91[EUR][1000 genomes]
rs240386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240388	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs240389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240390	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs240393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs240401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs240402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240404	0.91[EUR][1000 genomes]
rs240405	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs240409	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs240410	0.87[EUR][1000 genomes]
rs240423	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs240424	0.82[EUR][1000 genomes]
rs240429	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240430	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs240431	0.85[CEU][hapmap]
rs240432	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs2842455	0.82[YRI][hapmap]
rs381141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs397039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs414624	0.85[CEU][hapmap]
rs418485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs429746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs448854	0.91[EUR][1000 genomes]
rs507912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542717	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs638590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs643707	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs654428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs683943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6928694	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75917600-75946600	Weak transcription	Lung	lung
2	chr6:75918600-75920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:75918800-75919600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
4	chr6:75918800-75919800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:75918800-75920000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:75918800-75920600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:75918800-75920600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr6:75918800-75920800	Weak transcription	Fetal Muscle Leg	muscle
9	chr6:75918800-75920800	Weak transcription	Left Ventricle	heart
10	chr6:75918800-75920800	Weak transcription	Osteobl	bone
11	chr6:75918800-75921000	Weak transcription	Hela-S3	cervix
12	chr6:75918800-75921200	Weak transcription	A549	lung
13	chr6:75918800-75921400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr6:75918800-75921400	Weak transcription	HSMM	muscle
15	chr6:75918800-75921600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:75918800-75921600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:75918800-75921600	Weak transcription	Right Atrium	heart
18	chr6:75918800-75921600	Weak transcription	NH-A	brain
19	chr6:75918800-75921600	Weak transcription	NHEK	skin
20	chr6:75918800-75921600	Weak transcription	NHLF	lung
21	chr6:75918800-75921800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:75918800-75922000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:75918800-75922600	Weak transcription	Right Ventricle	heart
24	chr6:75918800-75924600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:75918800-75925000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr6:75918800-75925000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:75918800-75926400	Weak transcription	NHDF-Ad	bronchial
28	chr6:75918800-75926600	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:75918800-75926600	Weak transcription	Ovary	ovary
30	chr6:75918800-75926800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:75918800-75926800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr6:75919000-75920800	Weak transcription	Fetal Intestine Small	intestine
33	chr6:75919000-75921600	Weak transcription	HSMMtube	muscle
34	chr6:75919000-75924600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:75919200-75919600	Weak transcription	Fetal Lung	lung
36	chr6:75919200-75920200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:75919200-75920400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:75919200-75920600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:75919200-75925000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:75919400-75919600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr6:75919400-75921800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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