Variant report

Variant	rs11249665
Chromosome Location	chr5:179475818-179475819
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179474703..179477479-chr5:179497677..179500173,3	K562	blood:
2	chr5:179474524..179477374-chr5:179479073..179481485,2	MCF-7	breast:
3	chr5:179474365..179476555-chr5:179490686..179492434,2	MCF-7	breast:
4	chr5:179475261..179478154-chr5:179498153..179499999,2	MCF-7	breast:
5	chr5:179474557..179476078-chr5:179480075..179482538,2	MCF-7	breast:
6	chr5:179469293..179473403-chr5:179473812..179477504,5	MCF-7	breast:
7	chr5:179452407..179455273-chr5:179474700..179476534,2	K562	blood:
8	chr5:179469780..179472209-chr5:179474467..179476576,2	K562	blood:
9	chr5:179474733..179479669-chr5:179495487..179500173,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000113269	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10051694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10056316	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10056991	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[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10059400	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10066845	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071652	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10079029	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10464058	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11249663	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11249664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11249666	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11739706	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11739898	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11748441	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11750102	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[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435998	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17681274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278662	0.81[ASW][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs34585953	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3776946	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776948	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4235505	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700854	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700859	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4700864	0.83[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs57008562	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57117216	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61356660	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62404970	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62404974	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62404976	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404977	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404979	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62405015	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6601078	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861194	0.81[AMR][1000 genomes]
rs6862105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873317	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6884565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898203	1.00[ASW][hapmap];0.84[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.87[MKK][hapmap]
rs7729516	0.90[EUR][1000 genomes]
rs7734329	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9329095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats 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 miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11249665	CLTB	cis	parietal	SCAN
rs11249665	GRM6	cis	cerebellum	SCAN
rs11249665	C5orf45	cis	parietal	SCAN
rs11249665	RASGEF1C	cis	cerebellum	SCAN
rs11249665	PROP1	cis	parietal	SCAN
rs11249665	LTC4S	cis	cerebellum	SCAN
rs11249665	TRIM7	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179451200-179477200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:179462800-179477000	Weak transcription	Colonic Mucosa	Colon
5	chr5:179463800-179477000	Weak transcription	Small Intestine	intestine
6	chr5:179463800-179479200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:179464400-179476800	Weak transcription	HepG2	liver
9	chr5:179464400-179477200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:179465400-179477200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
13	chr5:179467400-179483200	Weak transcription	HSMM	muscle
14	chr5:179467800-179479000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:179468200-179477400	Weak transcription	A549	lung
16	chr5:179469000-179477000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr5:179471400-179476400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
19	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
20	chr5:179473400-179478000	Enhancers	Brain Hippocampus Middle	brain
21	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
22	chr5:179473600-179477600	Enhancers	Colon Smooth Muscle	Colon
23	chr5:179473600-179478000	Enhancers	Adipose Nuclei	Adipose
24	chr5:179473600-179479000	Weak transcription	Spleen	Spleen
25	chr5:179473800-179477200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:179473800-179477200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:179473800-179477200	Weak transcription	Brain Germinal Matrix	brain
28	chr5:179473800-179477400	Enhancers	Fetal Brain Male	brain
29	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
31	chr5:179474000-179476000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr5:179474000-179477000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:179474000-179477400	Enhancers	Primary hematopoietic stem cells	blood
34	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
35	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
36	chr5:179474200-179476000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:179474400-179476000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:179474400-179476400	Enhancers	Pancreas	Pancrea
39	chr5:179474600-179476000	Enhancers	Lung	lung
40	chr5:179474600-179476200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr5:179474600-179477400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr5:179474600-179477600	Enhancers	Brain Angular Gyrus	brain
43	chr5:179474600-179477800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:179474800-179476400	Enhancers	Right Ventricle	heart
45	chr5:179474800-179476600	Enhancers	Left Ventricle	heart
46	chr5:179474800-179476600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr5:179474800-179477200	Enhancers	Fetal Heart	heart
48	chr5:179474800-179477200	Enhancers	Fetal Lung	lung
49	chr5:179474800-179477800	Enhancers	Liver	Liver
50	chr5:179474800-179478000	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links