Variant report

Variant	rs2887998
Chromosome Location	chr12:56205389-56205390
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56202256..56204749-chr12:56204948..56206519,2	K562	blood:
2	chr12:56197510..56199937-chr12:56203851..56205706,2	MCF-7	breast:
3	chr12:56203945..56206681-chr12:56374371..56376076,2	MCF-7	breast:
4	chr12:56204184..56207939-chr12:56208091..56213011,15	K562	blood:
5	chr12:56131540..56134200-chr12:56203491..56206395,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205323	Chromatin interaction
ENSG00000123353	Chromatin interaction
ENSG00000237493	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10876851	0.94[ASW][hapmap];0.92[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes]
rs10876852	0.85[AMR][1000 genomes]
rs11171681	0.91[CHB][hapmap]
rs11829536	0.81[JPT][hapmap]
rs12372076	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs1681087	0.85[AMR][1000 genomes]
rs2291268	0.94[ASW][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap]
rs7305787	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs772262	1.00[ASW][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs7954619	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7954839	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs7965333	0.92[CHB][hapmap];0.90[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56144600-56208800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:56149400-56209600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56152800-56209000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:56160400-56209600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:56163200-56209400	Strong transcription	Fetal Thymus	thymus
6	chr12:56178800-56209200	Weak transcription	Stomach Mucosa	stomach
7	chr12:56183400-56210600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:56184800-56207800	Weak transcription	Fetal Heart	heart
9	chr12:56185000-56209400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:56187400-56208400	Weak transcription	Psoas Muscle	Psoas
11	chr12:56189600-56207600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr12:56189800-56208000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:56189800-56208800	Weak transcription	Fetal Brain Male	brain
14	chr12:56189800-56209600	Weak transcription	Brain Substantia Nigra	brain
15	chr12:56193200-56206400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:56193200-56207800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:56193200-56209200	Weak transcription	Colonic Mucosa	Colon
18	chr12:56195000-56209000	Weak transcription	HSMMtube	muscle
19	chr12:56195600-56206200	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:56195600-56209200	Weak transcription	Spleen	Spleen
21	chr12:56195600-56210600	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:56195800-56209200	Weak transcription	Brain Anterior Caudate	brain
23	chr12:56195800-56209600	Weak transcription	Fetal Kidney	kidney
24	chr12:56195800-56210200	Weak transcription	Aorta	Aorta
25	chr12:56196000-56205600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:56196000-56207800	Weak transcription	NHDF-Ad	bronchial
27	chr12:56196200-56206400	Weak transcription	NH-A	brain
28	chr12:56197200-56208800	Weak transcription	Brain Germinal Matrix	brain
29	chr12:56197600-56205600	Weak transcription	HSMM	muscle
30	chr12:56197600-56209000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr12:56198000-56208800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:56198000-56209200	Weak transcription	HMEC	breast
33	chr12:56198000-56209400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr12:56198400-56205400	Strong transcription	Fetal Intestine Small	intestine
35	chr12:56198600-56205800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:56199000-56205400	Strong transcription	Fetal Stomach	stomach
37	chr12:56199800-56205600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:56200600-56205400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:56200600-56205800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:56200600-56209400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:56201200-56206600	Weak transcription	GM12878-XiMat	blood
42	chr12:56201600-56207600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:56201800-56208800	Strong transcription	Primary B cells from peripheral blood	blood
44	chr12:56202000-56209600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:56202400-56205600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:56202400-56206400	Weak transcription	Hela-S3	cervix
47	chr12:56202400-56207800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:56202800-56207000	Weak transcription	Placenta	Placenta
49	chr12:56203000-56209200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:56203000-56209400	Weak transcription	Small Intestine	intestine

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