Variant report

Variant	rs1475195
Chromosome Location	chr13:52203295-52203296
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52166916..52169906-chr13:52201412..52203388,2	MCF-7	breast:
2	chr13:52202753..52205414-chr13:52302495..52304288,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242893	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1060562	0.86[ASN][1000 genomes]
rs12146894	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17532412	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597531	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885854	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2296028	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296029	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2897944	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3908968	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4555048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483879	0.94[CEU][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs488261	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs491103	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60757273	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199734	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526788	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9526793	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535714	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535715	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535717	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535722	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535734	0.86[ASN][1000 genomes]
rs9535735	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535738	0.89[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535739	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535744	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535746	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535747	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535748	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535749	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535750	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535753	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535756	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52189400-52205600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr13:52189400-52206600	Weak transcription	Primary B cells from cord blood	blood
3	chr13:52189400-52208800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:52190400-52205000	Enhancers	NHDF-Ad	bronchial
5	chr13:52192200-52204800	Enhancers	Brain Substantia Nigra	brain
6	chr13:52192400-52204000	Enhancers	HSMMtube	muscle
7	chr13:52192800-52205600	Weak transcription	A549	lung
8	chr13:52194200-52209400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:52194800-52205600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr13:52194800-52217600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:52195000-52205600	Enhancers	Muscle Satellite Cultured Cells	--
12	chr13:52196000-52207200	Weak transcription	Lung	lung
13	chr13:52196600-52206800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:52196800-52206200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr13:52196800-52206400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr13:52197600-52212400	Weak transcription	Fetal Kidney	kidney
17	chr13:52197800-52203800	Enhancers	Brain Anterior Caudate	brain
18	chr13:52197800-52206600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:52198000-52206600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr13:52198000-52209400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr13:52198400-52204200	Weak transcription	NHLF	lung
22	chr13:52198600-52217600	Weak transcription	Fetal Thymus	thymus
23	chr13:52198800-52203400	Enhancers	Brain Angular Gyrus	brain
24	chr13:52198800-52203400	Enhancers	Pancreas	Pancrea
25	chr13:52198800-52204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:52199000-52204200	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr13:52199200-52205600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:52199400-52204600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr13:52199400-52205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:52199400-52207000	Weak transcription	Aorta	Aorta
31	chr13:52199600-52205000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr13:52200000-52205800	Weak transcription	GM12878-XiMat	blood
33	chr13:52200200-52205800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr13:52200600-52207000	Weak transcription	Fetal Lung	lung
35	chr13:52200600-52209400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr13:52201200-52203600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:52201200-52205400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr13:52201200-52205600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:52201200-52207200	Weak transcription	Psoas Muscle	Psoas
40	chr13:52201200-52210800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr13:52201400-52203800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:52201400-52204200	Weak transcription	HSMM	muscle
43	chr13:52201400-52204200	Weak transcription	NHEK	skin
44	chr13:52201400-52205200	Weak transcription	HepG2	liver
45	chr13:52201400-52205600	Weak transcription	HMEC	breast
46	chr13:52201400-52205800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:52201400-52206600	Enhancers	Brain Hippocampus Middle	brain
48	chr13:52201400-52207000	Weak transcription	Ovary	ovary
49	chr13:52201400-52207200	Weak transcription	Gastric	stomach
50	chr13:52201600-52205600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links