Variant report

Variant	rs1885854
Chromosome Location	chr13:52313195-52313196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52158067..52160391-chr13:52310878..52313394,2	MCF-7	breast:
2	chr13:52024953..52028665-chr13:52311565..52316008,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224892	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000139668	Chromatin interaction
ENSG00000236778	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1060562	0.86[ASN][1000 genomes]
rs12146894	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12427748	1.00[CEU][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1475195	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17075907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17532412	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532524	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17532936	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17597215	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17597531	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2031993	1.00[MKK][hapmap]
rs2296028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296029	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2780461	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs2897944	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3908968	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs41292776	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4555048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs481133	1.00[ASW][hapmap]
rs483879	0.94[CEU][hapmap];0.87[JPT][hapmap];1.00[AFR][1000 genomes]
rs488261	1.00[AFR][1000 genomes]
rs491103	0.81[EUR][1000 genomes]
rs60757273	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199734	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73199746	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526783	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9526786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9526788	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9526793	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526794	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535714	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535715	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535717	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535722	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535735	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535737	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535738	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535741	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535743	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535744	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535745	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535746	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535747	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535748	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535750	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535751	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9535752	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535755	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9535756	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv455884	chr13:52302630-52405251	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv561644	chr13:52302630-52405251	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1885854	CKAP2	cis	parietal	SCAN
rs1885854	WDFY2	cis	parietal	SCAN
rs1885854	HNRNPA1L2	cis	parietal	SCAN
rs1885854	WDFY2	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52288400-52322200	Weak transcription	K562	blood
2	chr13:52296400-52322200	Weak transcription	Fetal Heart	heart
3	chr13:52298000-52322200	Weak transcription	Fetal Brain Female	brain
4	chr13:52300400-52322200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:52300600-52316000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr13:52300600-52321800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr13:52302200-52314000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:52302600-52313800	Weak transcription	Dnd41	blood
9	chr13:52302800-52313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr13:52302800-52313200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr13:52303400-52315000	Weak transcription	Fetal Thymus	thymus
12	chr13:52303800-52313600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr13:52304000-52320400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:52305000-52313200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:52305000-52313200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr13:52305000-52320400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:52305000-52338200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr13:52305200-52313200	Weak transcription	Placenta	Placenta
19	chr13:52305200-52320400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr13:52305400-52313800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr13:52305400-52315000	Weak transcription	Fetal Stomach	stomach
22	chr13:52305400-52321600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr13:52305400-52321800	Weak transcription	Gastric	stomach
24	chr13:52305600-52314800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr13:52305800-52322000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr13:52306000-52313200	Weak transcription	Fetal Lung	lung
27	chr13:52306000-52313200	Weak transcription	Pancreas	Pancrea
28	chr13:52306000-52314200	Weak transcription	NHLF	lung
29	chr13:52306000-52317800	Weak transcription	Small Intestine	intestine
30	chr13:52306000-52322200	Weak transcription	Left Ventricle	heart
31	chr13:52306000-52322200	Weak transcription	Right Ventricle	heart
32	chr13:52306200-52313200	Weak transcription	Brain Germinal Matrix	brain
33	chr13:52306200-52321400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr13:52306200-52339000	Weak transcription	Fetal Kidney	kidney
35	chr13:52306400-52320400	Weak transcription	Aorta	Aorta
36	chr13:52306600-52313200	Weak transcription	Ovary	ovary
37	chr13:52307800-52313200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr13:52308000-52313200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr13:52308000-52313200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr13:52308000-52313200	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:52308000-52313800	Weak transcription	Brain Hippocampus Middle	brain
42	chr13:52308000-52313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr13:52308000-52314400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr13:52308000-52314400	Weak transcription	Fetal Intestine Large	intestine
45	chr13:52308000-52315200	Weak transcription	Lung	lung
46	chr13:52308000-52316000	Strong transcription	HepG2	liver
47	chr13:52308000-52319000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:52308000-52322200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:52308200-52313200	Weak transcription	Adipose Nuclei	Adipose
50	chr13:52308200-52313800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links