Variant report

Variant	rs13198939
Chromosome Location	chr6:25179473-25179474
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	PBX3	chr6:25179277-25179861	SK-N-SH	brain:	n/a	n/a
2	SRF	chr6:25179231-25179532	GM12878	blood:	n/a	n/a
3	TCF12	chr6:25179215-25180092	SK-N-SH	brain:	n/a	n/a
4	MEF2C	chr6:25179371-25179760	GM12878	blood:	n/a	chr6:25179607-25179616 chr6:25179604-25179619 chr6:25179605-25179619 chr6:25179604-25179620 chr6:25179607-25179618 chr6:25179600-25179621 chr6:25179606-25179617 chr6:25179600-25179621 chr6:25179600-25179621
5	NFIC	chr6:25179248-25179988	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr6:25179336-25180021	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:25179400-25179835	SK-N-SH	brain:	n/a	n/a
8	ELK4	chr6:25179281-25179675	Hela-S3	cervix:	n/a	n/a
9	STAT1	chr6:25179354-25180164	Hela-S3	cervix:	n/a	chr6:25179595-25179602 chr6:25179775-25179786 chr6:25179776-25179785 chr6:25179774-25179788 chr6:25179771-25179791 chr6:25179788-25179796 chr6:25179777-25179786
10	MEF2A	chr6:25179436-25180022	SK-N-SH	brain:	n/a	chr6:25179607-25179616 chr6:25179604-25179619 chr6:25179605-25179619 chr6:25179604-25179620 chr6:25179607-25179618 chr6:25179600-25179621 chr6:25179606-25179617 chr6:25179600-25179621 chr6:25179600-25179621
11	FOSL2	chr6:25179441-25179937	SK-N-SH	brain:	n/a	chr6:25179707-25179719 chr6:25179710-25179721
12	FOXM1	chr6:25179062-25179952	SK-N-SH	brain:	n/a	n/a
13	ELK4	chr6:25179313-25179639	HEK293	kidney:	n/a	n/a
14	GATA3	chr6:25178845-25180100	SK-N-SH	brain:	n/a	n/a
15	SRF	chr6:25179353-25179518	GM12878	blood:	n/a	n/a
16	EP300	chr6:25179110-25179936	SK-N-SH	brain:	n/a	n/a
17	ELK1	chr6:25179312-25179662	Hela-S3	cervix:	n/a	n/a
18	MEF2A	chr6:25179279-25180046	SK-N-SH	brain:	n/a	chr6:25179607-25179616 chr6:25179604-25179619 chr6:25179605-25179619 chr6:25179604-25179620 chr6:25179607-25179618 chr6:25179600-25179621 chr6:25179606-25179617 chr6:25179600-25179621 chr6:25179600-25179621
19	GATA3	chr6:25179227-25179913	SK-N-SH	brain:	n/a	n/a
20	SRF	chr6:25179282-25179605	H1-hESC	embryonic stem cell:	n/a	n/a
21	TCF12	chr6:25179050-25180038	SK-N-SH	brain:	n/a	n/a
22	RXRA	chr6:25179286-25179923	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr6:25179227-25179831	IMR90	lung:	n/a	chr6:25179682-25179695

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25178331..25181085-chr6:25186884..25189706,2	MCF-7	breast:
2	chr6:25178946..25181215-chr6:27833164..27835187,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217805	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13198274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1815096	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs4144129	0.83[CEU][hapmap]
rs68094488	0.80[EUR][1000 genomes]
rs6938383	0.80[CEU][hapmap]

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	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1025694	chr6:25136860-25309450	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv1020774	chr6:25154152-25285679	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv538161	chr6:25154152-25285679	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv462663	chr6:25156197-25234884	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv601167	chr6:25156197-25234884	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25171600-25180000	Enhancers	Hela-S3	cervix
2	chr6:25175200-25192800	Weak transcription	Aorta	Aorta
3	chr6:25176200-25180000	Weak transcription	NH-A	brain
4	chr6:25176200-25180400	Weak transcription	Left Ventricle	heart
5	chr6:25176200-25192800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:25177000-25180400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:25177000-25180400	Weak transcription	Ovary	ovary
8	chr6:25177000-25181200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:25177000-25181800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:25177000-25182200	Weak transcription	NHEK	skin
11	chr6:25177000-25191800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:25177000-25194600	Weak transcription	Placenta	Placenta
13	chr6:25177200-25181600	Weak transcription	HMEC	breast
14	chr6:25177400-25181400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:25177600-25180600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr6:25177600-25182600	Enhancers	Primary hematopoietic stem cells	blood
17	chr6:25178000-25180800	Enhancers	HSMM	muscle
18	chr6:25178400-25180000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:25178600-25179600	Enhancers	Fetal Thymus	thymus
20	chr6:25178600-25179600	Enhancers	Thymus	Thymus
21	chr6:25178600-25179800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:25178600-25180000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr6:25178800-25179600	Enhancers	Fetal Stomach	stomach
24	chr6:25178800-25179600	Enhancers	GM12878-XiMat	blood
25	chr6:25178800-25180000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr6:25178800-25180000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:25178800-25180000	Enhancers	Stomach Smooth Muscle	stomach
28	chr6:25178800-25180000	Enhancers	NHLF	lung
29	chr6:25178800-25180800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:25178800-25181200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:25179000-25179600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:25179000-25179600	Enhancers	Primary B cells from peripheral blood	blood
33	chr6:25179000-25179600	Enhancers	Adipose Nuclei	Adipose
34	chr6:25179000-25179600	Flanking Active TSS	Colon Smooth Muscle	Colon
35	chr6:25179000-25179600	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr6:25179000-25179600	Enhancers	Fetal Muscle Leg	muscle
37	chr6:25179000-25179600	Flanking Active TSS	NHDF-Ad	bronchial
38	chr6:25179000-25181200	Enhancers	Osteobl	bone
39	chr6:25179000-25182600	Enhancers	Muscle Satellite Cultured Cells	--
40	chr6:25179000-25187000	Weak transcription	Spleen	Spleen
41	chr6:25179200-25179600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:25179200-25179600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:25179200-25179600	Enhancers	Fetal Brain Male	brain
44	chr6:25179200-25179600	Enhancers	Fetal Heart	heart
45	chr6:25179200-25179600	Flanking Active TSS	HSMMtube	muscle
46	chr6:25179200-25179800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:25179200-25179800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr6:25179200-25180000	Enhancers	Fetal Lung	lung
49	chr6:25179200-25180000	Enhancers	HUVEC	blood vessel
50	chr6:25179200-25181800	Enhancers	Primary neutrophils fromperipheralblood	blood

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