Variant report

Variant	rs13198274
Chromosome Location	chr6:25178990-25178991
allele	A/C
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	GATA3	chr6:25178724-25179074	T-47D	breast:	n/a	n/a
2	RUNX3	chr6:25178870-25179258	GM12878	blood:	n/a	n/a
3	GATA3	chr6:25178845-25180100	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr6:25178781-25179242	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:25178331..25181085-chr6:25186884..25189706,2	MCF-7	breast:
2	chr6:25178946..25181215-chr6:27833164..27835187,2	MCF-7	breast:
3	chr6:25175190..25179049-chr6:25180144..25182616,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217805	TF binding region
ENSG00000217805	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs13198544	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198939	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]
rs1815096	0.86[CEU][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs2328864	0.83[CEU][hapmap]
rs4144129	0.83[CEU][hapmap]
rs4711080	0.82[CEU][hapmap]
rs68094488	0.80[EUR][1000 genomes]
rs6938383	0.83[CEU][hapmap]
rs9393622	0.81[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13198274	GPLD1	cis	parietal	SCAN
rs13198274	HIST1H2BI	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25171600-25180000	Enhancers	Hela-S3	cervix
2	chr6:25174600-25179000	Weak transcription	Adipose Nuclei	Adipose
3	chr6:25174600-25179000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr6:25174600-25179200	Weak transcription	Fetal Lung	lung
5	chr6:25175200-25192800	Weak transcription	Aorta	Aorta
6	chr6:25175800-25179000	Enhancers	Colon Smooth Muscle	Colon
7	chr6:25175800-25179000	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:25175800-25179200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:25176200-25179000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr6:25176200-25180000	Weak transcription	NH-A	brain
11	chr6:25176200-25180400	Weak transcription	Left Ventricle	heart
12	chr6:25176200-25192800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:25176400-25179200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr6:25177000-25179200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:25177000-25179200	Weak transcription	HUVEC	blood vessel
16	chr6:25177000-25180400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:25177000-25180400	Weak transcription	Ovary	ovary
18	chr6:25177000-25181200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:25177000-25181800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:25177000-25182200	Weak transcription	NHEK	skin
21	chr6:25177000-25191800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:25177000-25194600	Weak transcription	Placenta	Placenta
23	chr6:25177200-25181600	Weak transcription	HMEC	breast
24	chr6:25177400-25179000	Weak transcription	Osteobl	bone
25	chr6:25177400-25181400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr6:25177600-25180600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:25177600-25182600	Enhancers	Primary hematopoietic stem cells	blood
28	chr6:25177800-25179200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:25178000-25180800	Enhancers	HSMM	muscle
30	chr6:25178400-25179000	Enhancers	NHDF-Ad	bronchial
31	chr6:25178400-25179200	Enhancers	HSMMtube	muscle
32	chr6:25178400-25180000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:25178600-25179000	Enhancers	Spleen	Spleen
34	chr6:25178600-25179400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr6:25178600-25179600	Enhancers	Fetal Thymus	thymus
36	chr6:25178600-25179600	Enhancers	Thymus	Thymus
37	chr6:25178600-25179800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:25178600-25180000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr6:25178800-25179000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:25178800-25179600	Enhancers	Fetal Stomach	stomach
41	chr6:25178800-25179600	Enhancers	GM12878-XiMat	blood
42	chr6:25178800-25180000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr6:25178800-25180000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:25178800-25180000	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:25178800-25180000	Enhancers	NHLF	lung
46	chr6:25178800-25180800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:25178800-25181200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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