Variant report

Variant	rs6427625
Chromosome Location	chr1:161718740-161718741
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:161718528-161718805	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:161717919-161718824	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161718394..161721019-chr17:57915124..57916843,2	MCF-7	breast:
2	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:
3	chr1:161703503..161707776-chr1:161717836..161724077,7	K562	blood:
4	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
5	chr1:161718380..161719915-chr8:144772917..144775501,2	MCF-7	breast:
6	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
7	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
8	chr1:161718255..161719858-chr8:127569641..127571490,2	MCF-7	breast:
9	chr1:161718427..161720383-chr1:161735445..161737521,2	MCF-7	breast:
10	chr1:161704696..161707209-chr1:161718366..161721899,3	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FCGR3B-7	chr1:161718366-161719580	NONHSAT007202

No data

Variant related genes	Relation type
DUSP12	TF binding region
ENSG00000226889	Chromatin interaction
ENSG00000241347	Chromatin interaction
ENSG00000168672	Chromatin interaction
ENSG00000181135	Chromatin interaction
ENSG00000254286	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000162746	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1027701	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1027702	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1063178	0.81[EUR][1000 genomes]
rs12026445	0.88[CHB][hapmap]
rs12116756	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12121310	0.81[EUR][1000 genomes]
rs12121522	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564653	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1340981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1417580	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1417581	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2066247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2174208	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4657096	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4657097	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4657098	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6427624	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427626	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540096	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161706800-161718800	Weak transcription	NH-A	brain
2	chr1:161707600-161719200	Weak transcription	NHLF	lung
3	chr1:161711400-161718800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:161714000-161718800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:161714000-161718800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:161714000-161718800	Weak transcription	HMEC	breast
7	chr1:161714000-161719000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:161714200-161718800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:161714400-161718800	Weak transcription	NHDF-Ad	bronchial
10	chr1:161714400-161718800	Weak transcription	Osteobl	bone
11	chr1:161714600-161718800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:161714600-161719000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:161714600-161719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:161714800-161719000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:161717400-161719200	Flanking Active TSS	GM12878-XiMat	blood
16	chr1:161717600-161719000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:161717600-161719200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr1:161717600-161719200	Enhancers	Primary B cells from peripheral blood	blood
19	chr1:161717600-161719200	Enhancers	HepG2	liver
20	chr1:161717600-161719400	Weak transcription	Lung	lung
21	chr1:161717800-161719200	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr1:161718200-161719000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:161718200-161719000	Enhancers	K562	blood
24	chr1:161718400-161718800	Enhancers	Dnd41	blood
25	chr1:161718400-161719000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:161718400-161719000	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:161718400-161719000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr1:161718400-161719000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr1:161718400-161719200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:161718400-161719200	Weak transcription	Placenta	Placenta
31	chr1:161718600-161718800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:161718600-161718800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:161718600-161718800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:161718600-161718800	Enhancers	Hela-S3	cervix
35	chr1:161718600-161719000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:161718600-161719000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:161718600-161719000	Enhancers	A549	lung
38	chr1:161718600-161719000	Enhancers	NHEK	skin
39	chr1:161718600-161719200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr1:161718600-161719200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:161718600-161719200	Enhancers	Brain Anterior Caudate	brain
42	chr1:161718600-161720200	Active TSS	Fetal Brain Male	brain

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