Variant report

Variant	rs6580824
Chromosome Location	chr12:51715349-51715350
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51475962..51477532-chr12:51714487..51716389,2	K562	blood:
2	chr12:51712710..51716828-chr12:51719754..51724043,5	K562	blood:
3	chr12:51438469..51440828-chr12:51713413..51715859,2	K562	blood:
4	chr12:51661913..51666807-chr12:51714627..51721165,8	MCF-7	breast:
5	chr12:51714696..51717509-chr12:51745471..51747033,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction
ENSG00000110925	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10876160	0.85[EUR][1000 genomes]
rs12228390	0.86[EUR][1000 genomes]
rs2288368	0.85[EUR][1000 genomes]
rs3843650	0.83[EUR][1000 genomes]
rs4435047	0.82[EUR][1000 genomes]
rs4761843	0.83[EUR][1000 genomes]
rs4761845	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4762035	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4762040	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4762042	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5029067	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7955476	0.85[EUR][1000 genomes]
rs7955688	0.85[EUR][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	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51708800-51716600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:51711200-51716800	Enhancers	Placenta	Placenta
3	chr12:51711800-51721800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:51712000-51717600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
5	chr12:51712200-51715600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr12:51712200-51716400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr12:51712400-51716200	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr12:51712400-51717400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:51712600-51715600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:51712800-51720200	Weak transcription	HMEC	breast
11	chr12:51713200-51715600	Weak transcription	Esophagus	oesophagus
12	chr12:51713200-51715800	Weak transcription	Small Intestine	intestine
13	chr12:51713200-51717000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:51713200-51717200	Weak transcription	Spleen	Spleen
15	chr12:51713200-51720000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:51713800-51716600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr12:51714000-51715400	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:51714000-51717000	Weak transcription	Fetal Muscle Trunk	muscle
19	chr12:51714200-51715600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:51714200-51715600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr12:51714200-51717800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:51714200-51718400	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr12:51714200-51718600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:51714400-51715400	Flanking Active TSS	Fetal Thymus	thymus
25	chr12:51714400-51715800	Enhancers	Fetal Lung	lung
26	chr12:51714400-51717200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr12:51714600-51715600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:51714600-51716000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:51714600-51716000	Flanking Active TSS	Dnd41	blood
30	chr12:51714600-51716200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:51714600-51717200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr12:51714800-51716400	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr12:51714800-51716800	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
34	chr12:51714800-51718200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:51715000-51715600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:51715000-51715600	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
37	chr12:51715000-51715600	Enhancers	A549	lung
38	chr12:51715000-51715800	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr12:51715000-51715800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr12:51715000-51716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr12:51715000-51716800	Weak transcription	Adipose Nuclei	Adipose
42	chr12:51715000-51716800	Weak transcription	Colonic Mucosa	Colon
43	chr12:51715000-51716800	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:51715000-51717200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr12:51715000-51717600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:51715000-51719000	Weak transcription	Stomach Mucosa	stomach
47	chr12:51715000-51720000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr12:51715000-51720000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:51715000-51720000	Weak transcription	Hela-S3	cervix
50	chr12:51715000-51720000	Weak transcription	HSMM	muscle

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