Variant report

Variant	rs11547281
Chromosome Location	chr2:87003846-87003847
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86995678..86997239-chr2:87001923..87004036,2	K562	blood:
2	chr2:87002968..87006528-chr2:87006846..87010010,3	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1018311	0.80[CHD][hapmap]
rs10186663	0.86[CHD][hapmap]
rs10201422	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs1049457	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs1049458	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs1051386	0.80[CEU][hapmap]
rs1193	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs12714203	0.84[ASN][1000 genomes]
rs12997796	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13004867	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13023213	0.86[CHB][hapmap]
rs13024420	0.86[CHB][hapmap]
rs13024609	0.86[CHB][hapmap]
rs13029597	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13297	0.84[ASN][1000 genomes]
rs1515950	0.86[CHB][hapmap]
rs1850138	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs1878109	0.86[CHD][hapmap]
rs2063848	0.86[CHD][hapmap]
rs2367378	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs2367379	0.84[ASN][1000 genomes]
rs2887012	0.86[CHD][hapmap]
rs3020728	0.81[ASN][1000 genomes]
rs3020729	0.80[CEU][hapmap]
rs34353387	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs34933869	0.88[ASN][1000 genomes]
rs35129240	0.88[ASN][1000 genomes]
rs35594332	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.88[ASN][1000 genomes]
rs35815787	0.88[ASN][1000 genomes]
rs3810831	0.86[CHB][hapmap]
rs4832311	0.86[CHD][hapmap]
rs4832312	0.84[ASN][1000 genomes]
rs6706378	0.84[ASN][1000 genomes]
rs6711696	0.84[ASN][1000 genomes]
rs6726451	0.88[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs6731890	0.86[CHD][hapmap]
rs67535255	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755452	0.86[CHB][hapmap]
rs67856656	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67864369	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558827	0.89[CEU][hapmap]
rs7561172	0.84[ASN][1000 genomes]
rs9309636	0.86[CHD][hapmap]
rs9309637	0.86[CHD][hapmap]
rs9309638	0.86[CHD][hapmap]
rs938486	0.88[CHB][hapmap];0.90[CHD][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv458585	chr2:86974318-87108211	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv582373	chr2:86974318-87108211	Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv1007307	chr2:86974563-87055214	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv535809	chr2:86974563-87055214	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1003748	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv535810	chr2:86975514-87032318	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
15	nsv1004572	chr2:86975514-87082883	Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
16	nsv535811	chr2:86975514-87082883	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11547281	RMND5A	cis	cerebellum	SCAN
rs11547281	TMEM150A	cis	cerebellum	SCAN
rs11547281	VPS24	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86974200-87004200	Weak transcription	Small Intestine	intestine
2	chr2:86975800-87006600	Weak transcription	NH-A	brain
3	chr2:86981400-87004600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:86981600-87007000	Weak transcription	NHDF-Ad	bronchial
5	chr2:86984200-87006000	Weak transcription	Ovary	ovary
6	chr2:86984600-87007600	Weak transcription	Psoas Muscle	Psoas
7	chr2:86988800-87006200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:86991600-87004600	Strong transcription	Primary B cells from cord blood	blood
9	chr2:86991800-87004200	Strong transcription	Primary T cells from cord blood	blood
10	chr2:86991800-87004600	Genic enhancers	Fetal Thymus	thymus
11	chr2:86992200-87004400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr2:86992200-87004400	Strong transcription	Dnd41	blood
13	chr2:86992200-87004600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:86992200-87004600	Strong transcription	Fetal Intestine Large	intestine
15	chr2:86992400-87004000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr2:86992400-87004400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr2:86992400-87004600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:86992400-87004800	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr2:86992600-87004000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr2:86992600-87004200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr2:86992600-87004200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr2:86992600-87004400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:86992600-87004600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:86992800-87004000	Strong transcription	Liver	Liver
25	chr2:86994600-87004400	Strong transcription	Primary B cells from peripheral blood	blood
26	chr2:86994600-87004400	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr2:86994800-87004200	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:86995400-87004000	Strong transcription	Esophagus	oesophagus
29	chr2:86995400-87004200	Strong transcription	GM12878-XiMat	blood
30	chr2:86995800-87004400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:86996400-87004200	Strong transcription	Adipose Nuclei	Adipose
32	chr2:86996400-87004400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:86997000-87004000	Strong transcription	NHEK	skin
34	chr2:86997000-87004400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:86997000-87004600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:86998200-87004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:86998200-87005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:86998200-87005800	Weak transcription	Right Ventricle	heart
39	chr2:86998200-87007000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:86998400-87005600	Weak transcription	Spleen	Spleen
41	chr2:86998400-87009000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:86998600-87007000	Weak transcription	Fetal Kidney	kidney
43	chr2:86998800-87004000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:86998800-87004400	Weak transcription	HUVEC	blood vessel
45	chr2:86998800-87008600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:86999200-87004400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:86999800-87004600	Strong transcription	Aorta	Aorta
48	chr2:87000000-87005800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:87000200-87005800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr2:87000200-87006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links