Variant report

Variant	rs11665980
Chromosome Location	chr19:18749354-18749355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18746749..18750617-chr19:18752436..18756057,4	K562	blood:
2	chr19:18703681..18707981-chr19:18746387..18750076,5	K562	blood:
3	chr19:18681104..18684544-chr19:18745683..18749906,4	K562	blood:
4	chr19:18698512..18700358-chr19:18745222..18750244,4	K562	blood:
5	chr19:18630375..18633112-chr19:18747617..18750132,3	K562	blood:
6	chr19:18700524..18703188-chr19:18747828..18749371,2	K562	blood:

Variant related genes	Relation type
ENSG00000105656	Chromatin interaction
ENSG00000167487	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000006016	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10424149	0.81[ASN][1000 genomes]
rs11667450	0.97[ASN][1000 genomes]
rs11668413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11670437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11672177	0.90[ASN][1000 genomes]
rs12972147	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12973480	0.85[CEU][hapmap];1.00[GIH][hapmap]
rs17683569	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs17683623	0.85[CEU][hapmap]
rs2238649	1.00[CHB][hapmap];0.91[CHD][hapmap]
rs35322184	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[ASN][1000 genomes]
rs3752217	0.91[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3752218	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3764628	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795027	0.80[CHD][hapmap]
rs61248595	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66840797	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs66969630	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs68074367	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72997346	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997355	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs752981	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8107912	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs8108207	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription 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 target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv3332947	chr19:18745902-18749700	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11665980	TSSK6	cis	parietal	SCAN
rs11665980	CRLF1	cis	parietal	SCAN
rs11665980	TMEM59L	cis	cerebellum	SCAN
rs11665980	CYP4F12	cis	cerebellum	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18747800-18749400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:18748000-18749400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
3	chr19:18748200-18749400	Flanking Active TSS	Dnd41	blood
4	chr19:18748400-18749400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:18748400-18749400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:18748400-18749400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:18748400-18749400	Enhancers	Esophagus	oesophagus
8	chr19:18748400-18749400	Enhancers	Gastric	stomach
9	chr19:18748400-18749400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr19:18748400-18749400	Enhancers	Stomach Mucosa	stomach
11	chr19:18748400-18749400	Flanking Active TSS	HepG2	liver
12	chr19:18748400-18749800	Enhancers	Spleen	Spleen
13	chr19:18748400-18761600	Weak transcription	Aorta	Aorta
14	chr19:18748600-18749400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:18748600-18749400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:18748600-18749400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr19:18748600-18749400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr19:18748600-18749400	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr19:18748600-18749400	Enhancers	Colonic Mucosa	Colon
20	chr19:18748600-18749400	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr19:18748600-18749400	Flanking Active TSS	GM12878-XiMat	blood
22	chr19:18748600-18749400	Flanking Active TSS	Hela-S3	cervix
23	chr19:18748600-18749600	Enhancers	Fetal Intestine Small	intestine
24	chr19:18748600-18755800	Weak transcription	Ovary	ovary
25	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:18748800-18749400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr19:18748800-18749400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr19:18748800-18749400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:18748800-18749400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr19:18748800-18749400	Enhancers	Liver	Liver
31	chr19:18748800-18749400	Flanking Active TSS	Brain Anterior Caudate	brain
32	chr19:18748800-18749400	Enhancers	Brain Hippocampus Middle	brain
33	chr19:18748800-18749400	Enhancers	Fetal Intestine Large	intestine
34	chr19:18748800-18749400	Enhancers	Lung	lung
35	chr19:18748800-18749400	Enhancers	Psoas Muscle	Psoas
36	chr19:18748800-18749400	Enhancers	Right Ventricle	heart
37	chr19:18748800-18749600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:18748800-18749800	Enhancers	Pancreas	Pancrea
39	chr19:18748800-18751000	Weak transcription	Fetal Stomach	stomach
40	chr19:18748800-18754800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:18748800-18757400	Weak transcription	Fetal Kidney	kidney
42	chr19:18748800-18758600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:18748800-18759200	Weak transcription	Fetal Lung	lung
44	chr19:18749000-18749400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr19:18749000-18749400	Enhancers	Adipose Nuclei	Adipose
46	chr19:18749000-18749400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:18749000-18749400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr19:18749000-18749400	Enhancers	Fetal Brain Female	brain
49	chr19:18749000-18749400	Enhancers	Left Ventricle	heart
50	chr19:18749000-18749400	Enhancers	Right Atrium	heart

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