Variant report

Variant	rs3212829
Chromosome Location	chr19:51323913-51323914
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:51314145..51316152-chr19:51321518..51323994,2	MCF-7	breast:
2	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
3	chr19:51321294..51329149-chr19:51334672..51341529,13	K562	blood:

Variant related genes	Relation type
ENSG00000167747	Chromatin interaction
ENSG00000174562	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10421200	0.96[EUR][1000 genomes]
rs3212808	0.90[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212814	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212815	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212830	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212842	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212844	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3212847	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3212858	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36217621	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5514	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5515	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7259922	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8102269	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv524637	chr19:51321083-51332670	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv523089	chr19:51321083-51336197	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51320800-51338800	Weak transcription	Right Atrium	heart
2	chr19:51321400-51324000	Flanking Active TSS	GM12878-XiMat	blood
3	chr19:51321800-51327600	Enhancers	Primary B cells from peripheral blood	blood
4	chr19:51322200-51324400	Bivalent/Poised TSS	Colonic Mucosa	Colon
5	chr19:51322400-51324200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
6	chr19:51323000-51324200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
7	chr19:51323000-51324200	Flanking Active TSS	K562	blood
8	chr19:51323200-51324000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
9	chr19:51323200-51324000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:51323200-51324600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr19:51323200-51324800	Bivalent Enhancer	Fetal Thymus	thymus
12	chr19:51323200-51324800	Active TSS	Pancreas	Pancrea
13	chr19:51323400-51324000	Bivalent Enhancer	Thymus	Thymus
14	chr19:51323400-51324400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:51323400-51324600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
16	chr19:51323400-51324600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
17	chr19:51323400-51324600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
18	chr19:51323400-51324600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr19:51323400-51324800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
20	chr19:51323400-51324800	Enhancers	Esophagus	oesophagus
21	chr19:51323400-51325200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
22	chr19:51323600-51324000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
23	chr19:51323600-51324000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:51323600-51324000	Bivalent Enhancer	A549	lung
25	chr19:51323600-51324200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr19:51323600-51324200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:51323600-51324200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
28	chr19:51323600-51324400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr19:51323600-51324400	Active TSS	Duodenum Mucosa	Duodenum
30	chr19:51323600-51324600	Active TSS	H9 Cell Line	embryonic stem cell
31	chr19:51323600-51324600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:51323600-51325000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr19:51323600-51325200	Enhancers	Primary B cells from cord blood	blood
34	chr19:51323600-51325800	Bivalent Enhancer	Fetal Intestine Large	intestine
35	chr19:51323800-51324000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
36	chr19:51323800-51324000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
37	chr19:51323800-51324000	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
38	chr19:51323800-51324000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr19:51323800-51324000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:51323800-51324000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:51323800-51324000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
42	chr19:51323800-51324000	Bivalent Enhancer	Fetal Heart	heart
43	chr19:51323800-51324000	Bivalent Enhancer	Fetal Lung	lung
44	chr19:51323800-51324000	Flanking Bivalent TSS/Enh	Stomach Mucosa	stomach
45	chr19:51323800-51324200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:51323800-51324200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:51323800-51324200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:51323800-51324400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
49	chr19:51323800-51324600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr19:51323800-51324600	Bivalent Enhancer	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links