Variant report

Variant	rs61544138
Chromosome Location	chr6:75811857-75811858
allele	C/T
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	MAFK	chr6:75811627-75812355	IMR90	lung:	n/a	n/a
2	POLR2A	chr6:75811492-75811921	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr6:75811504-75811976	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr6:75811615-75811919	HUVEC	blood vessel:	n/a	n/a
5	JUN	chr6:75811294-75812000	HUVEC	blood vessel:	n/a	chr6:75811833-75811842
6	GATA2	chr6:75811580-75812461	HUVEC	blood vessel:	n/a	n/a
7	FOS	chr6:75811702-75811902	MCF10A-Er-Src	breast:	n/a	chr6:75811831-75811842 chr6:75811833-75811842
8	JUND	chr6:75811755-75811904	HepG2	liver:	n/a	chr6:75811831-75811842 chr6:75811833-75811842
9	FOS	chr6:75811729-75811900	MCF10A-Er-Src	breast:	n/a	chr6:75811831-75811842 chr6:75811833-75811842
10	FOS	chr6:75811448-75812364	HUVEC	blood vessel:	n/a	chr6:75811831-75811842 chr6:75811833-75811842
11	RAD21	chr6:75811554-75811932	IMR90	lung:	n/a	n/a
12	CEBPB	chr6:75811622-75811987	IMR90	lung:	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:46)

rs_ID	r²[population]
rs10046165	1.00[EUR][1000 genomes]
rs10046211	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10223595	1.00[EUR][1000 genomes]
rs10943232	1.00[EUR][1000 genomes]
rs10943233	1.00[EUR][1000 genomes]
rs11964481	1.00[EUR][1000 genomes]
rs35227190	1.00[EUR][1000 genomes]
rs35710072	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36002196	1.00[EUR][1000 genomes]
rs4235892	1.00[EUR][1000 genomes]
rs4266465	1.00[EUR][1000 genomes]
rs4292495	1.00[EUR][1000 genomes]
rs4473827	1.00[EUR][1000 genomes]
rs56118316	1.00[EUR][1000 genomes]
rs56978570	1.00[EUR][1000 genomes]
rs58333285	1.00[EUR][1000 genomes]
rs61413320	1.00[EUR][1000 genomes]
rs6453794	1.00[EUR][1000 genomes]
rs6453814	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6903588	1.00[EUR][1000 genomes]
rs6906046	1.00[EUR][1000 genomes]
rs6907120	1.00[EUR][1000 genomes]
rs6909123	1.00[EUR][1000 genomes]
rs6911004	1.00[EUR][1000 genomes]
rs6920790	1.00[EUR][1000 genomes]
rs6921378	1.00[EUR][1000 genomes]
rs6931257	1.00[EUR][1000 genomes]
rs7754758	1.00[EUR][1000 genomes]
rs7766168	1.00[EUR][1000 genomes]
rs7772904	1.00[EUR][1000 genomes]
rs9293993	1.00[EUR][1000 genomes]
rs9293994	1.00[EUR][1000 genomes]
rs9293995	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9293996	1.00[EUR][1000 genomes]
rs9352183	1.00[EUR][1000 genomes]
rs9443130	1.00[EUR][1000 genomes]
rs9443133	1.00[EUR][1000 genomes]
rs9443135	1.00[EUR][1000 genomes]
rs9443151	1.00[EUR][1000 genomes]
rs9443152	1.00[EUR][1000 genomes]
rs9447409	1.00[EUR][1000 genomes]
rs9447441	1.00[EUR][1000 genomes]
rs9447443	1.00[EUR][1000 genomes]
rs9447444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9447446	1.00[EUR][1000 genomes]
rs9447448	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75800400-75815600	Genic enhancers	Osteobl	bone
2	chr6:75802400-75813600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:75804600-75814400	Genic enhancers	NHLF	lung
4	chr6:75806600-75818600	Strong transcription	NHEK	skin
5	chr6:75806800-75814000	Genic enhancers	NHDF-Ad	bronchial
6	chr6:75806800-75816000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:75808400-75826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:75808600-75812800	Weak transcription	Fetal Intestine Large	intestine
9	chr6:75808800-75818200	Weak transcription	Aorta	Aorta
10	chr6:75809000-75819600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:75809000-75824600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:75809200-75815000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:75809400-75812200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:75809400-75816800	Strong transcription	HMEC	breast
15	chr6:75809600-75813600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:75809600-75815400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:75809600-75828200	Weak transcription	Hela-S3	cervix
18	chr6:75809600-75862000	Weak transcription	Fetal Kidney	kidney
19	chr6:75809800-75812400	Strong transcription	Stomach Smooth Muscle	stomach
20	chr6:75809800-75813200	Strong transcription	Fetal Stomach	stomach
21	chr6:75809800-75814600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr6:75809800-75816600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:75809800-75818600	Strong transcription	HSMMtube	muscle
24	chr6:75810000-75844400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr6:75810200-75812000	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:75810200-75812800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:75810200-75813400	Strong transcription	Fetal Muscle Leg	muscle
28	chr6:75810200-75815800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:75810200-75816400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:75811000-75812600	Enhancers	HUVEC	blood vessel
31	chr6:75811200-75812000	Strong transcription	Fetal Intestine Small	intestine
32	chr6:75811200-75814600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:75811200-75816200	Strong transcription	Colon Smooth Muscle	Colon
34	chr6:75811400-75812800	Enhancers	NH-A	brain
35	chr6:75811400-75813600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:75811600-75812200	Strong transcription	Ovary	ovary
37	chr6:75811600-75812400	Genic enhancers	HSMM	muscle
38	chr6:75811600-75812600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:75811600-75813200	Genic enhancers	Placenta Amnion	Placenta Amnion
40	chr6:75811800-75813000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:75811800-75813000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links