Variant report

Variant	rs688253
Chromosome Location	chr3:100321689-100321690
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100321003..100323549-chr3:100347554..100350487,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1165522	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs11921235	0.91[AMR][1000 genomes]
rs1305376	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1305377	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1305378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1676368	0.84[AMR][1000 genomes]
rs1676370	0.84[AMR][1000 genomes]
rs1676371	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1718269	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1718270	0.84[AMR][1000 genomes]
rs1718271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs528097	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57295454	0.91[AMR][1000 genomes]
rs57379878	0.91[AMR][1000 genomes]
rs57518757	0.91[AMR][1000 genomes]
rs57865794	0.91[AMR][1000 genomes]
rs60148175	0.91[AMR][1000 genomes]
rs61179072	0.91[AMR][1000 genomes]
rs667277	0.91[AMR][1000 genomes]
rs6806901	0.91[AMR][1000 genomes]
rs7431884	0.91[AMR][1000 genomes]
rs7431911	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2756284	chr3:100299329-100427937	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752830	chr3:100299329-100442478	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv432464	chr3:100299329-100442478	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv536667	chr3:100308355-100445857	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv460770	chr3:100310812-100433592	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv591150	chr3:100310812-100433592	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv2763708	chr3:100317928-100442509	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100318200-100324200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:100318800-100323200	Enhancers	HMEC	breast
3	chr3:100319000-100323000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:100319400-100322000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:100319400-100322200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:100319600-100321800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:100319600-100322000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:100319600-100322000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:100319600-100322000	Weak transcription	Thymus	Thymus
10	chr3:100319800-100321800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr3:100319800-100322000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:100319800-100322200	Weak transcription	Fetal Thymus	thymus
13	chr3:100319800-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:100320000-100322600	Weak transcription	Esophagus	oesophagus
15	chr3:100320200-100322800	Enhancers	NHEK	skin
16	chr3:100320400-100322200	Enhancers	Liver	Liver
17	chr3:100320600-100321800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:100320600-100323000	Enhancers	Fetal Intestine Small	intestine
19	chr3:100320800-100323000	Enhancers	Fetal Intestine Large	intestine
20	chr3:100321000-100322600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:100321000-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:100321200-100321800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:100321200-100321800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr3:100321200-100321800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:100321200-100321800	Enhancers	NHLF	lung
26	chr3:100321200-100322200	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:100321200-100322400	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:100321200-100322400	Flanking Active TSS	HepG2	liver
29	chr3:100321200-100322600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:100321200-100322600	Enhancers	Hela-S3	cervix
31	chr3:100321200-100322600	Enhancers	NHDF-Ad	bronchial
32	chr3:100321200-100322800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:100321200-100322800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr3:100321200-100322800	Enhancers	Stomach Mucosa	stomach
35	chr3:100321200-100322800	Enhancers	HSMMtube	muscle
36	chr3:100321200-100322800	Enhancers	K562	blood
37	chr3:100321200-100323000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr3:100321400-100321800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr3:100321400-100321800	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr3:100321400-100321800	Enhancers	Primary hematopoietic stem cells	blood
41	chr3:100321400-100321800	Enhancers	Adipose Nuclei	Adipose
42	chr3:100321400-100321800	Flanking Active TSS	GM12878-XiMat	blood
43	chr3:100321400-100321800	Enhancers	Osteobl	bone
44	chr3:100321400-100322000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:100321400-100322000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:100321400-100322000	Enhancers	HSMM	muscle
47	chr3:100321400-100322600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:100321400-100322800	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr3:100321400-100322800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr3:100321400-100322800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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