Variant report

Variant	rs11024625
Chromosome Location	chr11:18371560-18371561
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	chr11:18363673..18366385-chr11:18369468..18372375,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11024605	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024607	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024611	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024619	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024621	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024632	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12221676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12224608	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1869786	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1869787	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3781944	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150530	0.92[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4150572	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150606	0.84[JPT][hapmap]
rs4150626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150628	0.84[JPT][hapmap]
rs4150635	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4150656	0.86[AFR][1000 genomes]
rs4150658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237721	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344464	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4366463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4586132	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756938	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757639	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757642	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4757645	1.00[YRI][hapmap]
rs4757646	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60677587	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7113249	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7122032	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128017	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128146	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73430865	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73430866	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73430881	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73430888	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73430894	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73432712	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73434649	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11024625	NUCB2	cis	cerebellum	SCAN
rs11024625	HPS5	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:18346800-18372000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:18347000-18372400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr11:18350400-18372000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr11:18350400-18372000	Strong transcription	Liver	Liver
10	chr11:18350600-18371600	Strong transcription	Fetal Intestine Large	intestine
11	chr11:18350800-18371800	Strong transcription	Fetal Muscle Leg	muscle
12	chr11:18350800-18372200	Strong transcription	Placenta	Placenta
13	chr11:18351200-18373600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
15	chr11:18351600-18371800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:18352400-18371600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:18353200-18372200	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:18353800-18372000	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:18354000-18371800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr11:18354000-18372200	Strong transcription	Adipose Nuclei	Adipose
22	chr11:18354400-18371600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:18354400-18371800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr11:18354400-18371800	Strong transcription	HSMM	muscle
25	chr11:18354400-18372000	Strong transcription	Duodenum Mucosa	Duodenum
26	chr11:18354400-18389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:18355000-18372000	Strong transcription	Primary B cells from cord blood	blood
28	chr11:18355600-18372000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:18357000-18389200	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr11:18357200-18379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr11:18357400-18371800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:18359200-18374200	Weak transcription	Psoas Muscle	Psoas
33	chr11:18360000-18382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:18360200-18374400	Weak transcription	Small Intestine	intestine
35	chr11:18361800-18391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr11:18362400-18374400	Weak transcription	Aorta	Aorta
37	chr11:18363000-18390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:18363200-18379400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
40	chr11:18364800-18372000	Strong transcription	Brain Germinal Matrix	brain
41	chr11:18365200-18372000	Strong transcription	Primary T cells from cord blood	blood
42	chr11:18365800-18381400	Weak transcription	Pancreas	Pancrea
43	chr11:18366600-18381400	Weak transcription	Gastric	stomach
44	chr11:18367000-18372000	Strong transcription	Left Ventricle	heart
45	chr11:18367000-18372000	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr11:18367200-18375400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr11:18367600-18371800	Strong transcription	Brain Substantia Nigra	brain
48	chr11:18367600-18390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr11:18368000-18376000	Weak transcription	Right Ventricle	heart
50	chr11:18368000-18382400	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links