Variant report

Variant	rs11688481
Chromosome Location	chr2:48558619-48558620
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48550065..48552046-chr2:48557575..48559707,2	MCF-7	breast:
2	chr2:48558442..48561276-chr2:48561458..48563692,2	K562	blood:
3	chr2:48517525..48519074-chr2:48557962..48560768,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.87[ASN][1000 genomes]
rs10199431	0.87[JPT][hapmap]
rs10454133	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs10454134	0.83[JPT][hapmap];1.00[YRI][hapmap]
rs10495951	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.87[ASN][1000 genomes]
rs10495952	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11676036	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11676168	0.91[JPT][hapmap]
rs11678403	0.83[ASN][1000 genomes]
rs11679523	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap]
rs11680916	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11682044	0.83[JPT][hapmap]
rs11682633	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11683099	0.87[ASN][1000 genomes]
rs11683639	0.81[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap]
rs11684517	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11685861	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11686007	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11687708	0.86[ASN][1000 genomes]
rs11689622	0.90[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap]
rs11689645	0.86[ASN][1000 genomes]
rs11690690	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11690748	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11690845	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12052754	0.88[ASN][1000 genomes]
rs12328506	0.88[ASN][1000 genomes]
rs13388291	0.86[JPT][hapmap]
rs13398791	0.88[ASN][1000 genomes]
rs13401749	0.90[GIH][hapmap];0.87[JPT][hapmap];0.89[MEX][hapmap]
rs13432998	0.87[JPT][hapmap]
rs17037289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17037298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17397449	1.00[YRI][hapmap]
rs17855177	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4411759	0.87[JPT][hapmap]
rs4438532	0.83[JPT][hapmap]
rs4547570	0.88[ASN][1000 genomes]
rs4606978	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap]
rs55660911	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55744465	0.85[ASN][1000 genomes]
rs55761545	0.99[ASN][1000 genomes]
rs55788229	0.85[ASN][1000 genomes]
rs56156294	0.85[ASN][1000 genomes]
rs56163539	0.82[ASN][1000 genomes]
rs56391806	0.85[ASN][1000 genomes]
rs57131168	0.90[ASN][1000 genomes]
rs57537506	0.94[ASN][1000 genomes]
rs57893565	0.90[ASN][1000 genomes]
rs58012056	0.92[ASN][1000 genomes]
rs59697023	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60815228	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60825643	0.87[ASN][1000 genomes]
rs62137015	0.91[ASN][1000 genomes]
rs6545027	0.82[JPT][hapmap]
rs6545030	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6545036	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6705802	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6712029	0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6718068	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6722246	0.92[ASN][1000 genomes]
rs6743757	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6745580	0.94[ASN][1000 genomes]
rs6756596	0.89[ASN][1000 genomes]
rs72818478	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72818488	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72818491	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72818494	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72818502	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820403	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72820404	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820409	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820411	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820415	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820416	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72820418	0.93[ASN][1000 genomes]
rs72820420	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820422	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820423	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820424	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72820427	0.90[ASN][1000 genomes]
rs72820433	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72820436	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72820437	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820439	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72820441	0.88[ASN][1000 genomes]
rs72820445	0.92[ASN][1000 genomes]
rs7559431	0.86[ASN][1000 genomes]
rs7562069	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7562816	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7566239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7573316	0.92[ASN][1000 genomes]
rs7576964	0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7577237	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7579932	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7600794	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7606104	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv519831	chr2:48072855-48566031	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1003766	chr2:48102244-48559654	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11688481	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48543400-48568600	Weak transcription	HSMM	muscle
2	chr2:48543600-48559400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr2:48543600-48561000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:48543600-48570600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr2:48544200-48559600	Weak transcription	Fetal Kidney	kidney
6	chr2:48544400-48570400	Weak transcription	NHEK	skin
7	chr2:48544400-48570800	Weak transcription	HMEC	breast
8	chr2:48544600-48564400	Weak transcription	Fetal Intestine Small	intestine
9	chr2:48544800-48559400	Weak transcription	Right Atrium	heart
10	chr2:48548600-48570600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:48550400-48562200	Enhancers	Brain Substantia Nigra	brain
12	chr2:48550600-48559400	Enhancers	Brain Hippocampus Middle	brain
13	chr2:48552000-48558800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr2:48552400-48561000	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr2:48552400-48561600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:48552400-48566200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:48552400-48570600	Weak transcription	Aorta	Aorta
18	chr2:48553400-48574400	Weak transcription	Lung	lung
19	chr2:48553800-48570800	Weak transcription	Thymus	Thymus
20	chr2:48554400-48561000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr2:48554400-48570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:48554800-48561600	Weak transcription	Psoas Muscle	Psoas
23	chr2:48554800-48562000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr2:48555000-48560400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:48555000-48560400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr2:48555000-48561600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr2:48555000-48562000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:48555200-48559000	Enhancers	Brain Cingulate Gyrus	brain
29	chr2:48555200-48560800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr2:48555400-48558800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:48555400-48558800	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr2:48555400-48570600	Weak transcription	NHLF	lung
33	chr2:48556000-48560400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr2:48556800-48558800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:48556800-48559600	Weak transcription	HSMMtube	muscle
36	chr2:48556800-48559800	Enhancers	Brain Anterior Caudate	brain
37	chr2:48556800-48560400	Enhancers	Primary B cells from cord blood	blood
38	chr2:48556800-48562800	Enhancers	Brain Angular Gyrus	brain
39	chr2:48556800-48570600	Weak transcription	Fetal Thymus	thymus
40	chr2:48556800-48571600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:48557000-48559000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr2:48557000-48559000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr2:48557000-48559200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:48557000-48560200	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr2:48557000-48566600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:48557000-48567600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr2:48557000-48573200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:48557000-48573400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:48557200-48559400	Weak transcription	Adipose Nuclei	Adipose
50	chr2:48557200-48564400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links