Variant report

Variant	rs12328646
Chromosome Location	chr2:145082658-145082659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:145081859..145086647-chr2:145087025..145090343,4	MCF-7	breast:
2	chr2:145080448..145086688-chr2:145086871..145092825,10	K562	blood:

Variant related genes	Relation type
ENSG00000121964	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10183920	0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11886379	0.85[YRI][hapmap]
rs13404324	1.00[MEX][hapmap]
rs13425139	0.86[ASW][hapmap]
rs1427654	0.80[ASW][hapmap]
rs16823453	1.00[EUR][1000 genomes]
rs16823456	1.00[EUR][1000 genomes]
rs16823477	1.00[EUR][1000 genomes]
rs16823483	1.00[EUR][1000 genomes]
rs16823486	1.00[EUR][1000 genomes]
rs16823490	1.00[EUR][1000 genomes]
rs16823495	1.00[EUR][1000 genomes]
rs16823544	1.00[TSI][hapmap]
rs16823583	0.82[LWK][hapmap]
rs16823609	1.00[TSI][hapmap]
rs58046208	1.00[EUR][1000 genomes]
rs59638652	1.00[EUR][1000 genomes]
rs6430049	1.00[EUR][1000 genomes]
rs6709167	1.00[EUR][1000 genomes]
rs6733058	1.00[EUR][1000 genomes]
rs6736292	1.00[EUR][1000 genomes]
rs6747751	1.00[EUR][1000 genomes]
rs6758720	0.97[LWK][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs72992116	1.00[EUR][1000 genomes]
rs73006242	1.00[EUR][1000 genomes]
rs73006264	1.00[EUR][1000 genomes]
rs73006270	1.00[EUR][1000 genomes]
rs73006274	1.00[EUR][1000 genomes]
rs73006276	1.00[EUR][1000 genomes]
rs73006279	1.00[EUR][1000 genomes]
rs73964986	1.00[EUR][1000 genomes]
rs7588281	0.82[AFR][1000 genomes]
rs7595013	1.00[TSI][hapmap]
rs997840	0.82[AFR][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	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking 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 lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv532756	chr2:144746353-145315596	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv1008032	chr2:144840552-145234229	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv997624	chr2:144906679-145294503	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
9	nsv535952	chr2:144906679-145294503	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
10	nsv532757	chr2:144922143-145263446	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
11	nsv916172	chr2:144970681-145425713	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv948474	chr2:145035890-145436665	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised 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	14 gene(s)	inside rSNPs	diseases
13	nsv1004937	chr2:145079535-145159021	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:145070800-145088000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:145075000-145088400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:145078400-145084400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:145078400-145088600	Weak transcription	Ovary	ovary
5	chr2:145078400-145088600	Weak transcription	Right Ventricle	heart
6	chr2:145078400-145089200	Weak transcription	Spleen	Spleen
7	chr2:145078600-145085400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:145078600-145088400	Weak transcription	HSMM	muscle
9	chr2:145078800-145085200	Weak transcription	Psoas Muscle	Psoas
10	chr2:145078800-145088600	Weak transcription	HSMMtube	muscle
11	chr2:145079000-145088600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:145079600-145082800	Weak transcription	Right Atrium	heart
13	chr2:145079800-145082800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:145080400-145088200	Weak transcription	Brain Germinal Matrix	brain
15	chr2:145080800-145083000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:145080800-145089000	Weak transcription	Lung	lung
17	chr2:145081000-145083600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:145081000-145083600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:145081000-145083600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:145081000-145087400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:145081000-145088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:145081200-145083400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:145081200-145083600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:145081200-145087400	Weak transcription	Fetal Lung	lung
25	chr2:145081400-145082800	Enhancers	Primary B cells from cord blood	blood
26	chr2:145081400-145083000	Enhancers	Primary B cells from peripheral blood	blood
27	chr2:145081400-145083000	Enhancers	NHEK	skin
28	chr2:145081600-145087800	Weak transcription	NHDF-Ad	bronchial
29	chr2:145081800-145083000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:145081800-145083400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:145081800-145087000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:145082000-145082800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:145082000-145082800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:145082000-145082800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:145082000-145082800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:145082000-145082800	Enhancers	HMEC	breast
37	chr2:145082000-145083000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:145082000-145083000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:145082000-145083200	Enhancers	Fetal Kidney	kidney
40	chr2:145082000-145083200	Enhancers	A549	lung
41	chr2:145082000-145083400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr2:145082000-145083400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr2:145082000-145083400	Enhancers	Fetal Heart	heart
44	chr2:145082200-145082800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr2:145082200-145082800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr2:145082200-145083000	Enhancers	Brain Hippocampus Middle	brain
47	chr2:145082200-145083000	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:145082200-145083200	Enhancers	Primary T cells from cord blood	blood
49	chr2:145082200-145083400	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr2:145082200-145083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links