Variant report

Variant	rs6506520
Chromosome Location	chr18:7627956-7627957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10153440	0.81[ASN][1000 genomes]
rs11877002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1446080	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1664983	0.90[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16952257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16952260	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1893223	0.83[ASW][hapmap]
rs1940347	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1941136	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2032176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2032177	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28470267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28750977	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28788217	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55750787	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6506523	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6506524	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6650627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6650628	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7228736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7233631	1.00[ASW][hapmap]
rs9946325	0.91[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9955885	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9956880	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9961570	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9961754	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2656232	chr18:7111033-7658679	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1064597	chr18:7169490-7762738	Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv543636	chr18:7169490-7762738	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1063350	chr18:7215275-7659999	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking 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	6 gene(s)	inside rSNPs	diseases
5	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6506520	SNORD116-29	trans	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7620000-7632000	Weak transcription	Fetal Kidney	kidney
2	chr18:7620400-7633400	Weak transcription	Aorta	Aorta
3	chr18:7620600-7632400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr18:7624200-7629000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr18:7625800-7628000	Enhancers	Left Ventricle	heart
6	chr18:7625800-7628200	Enhancers	Right Atrium	heart
7	chr18:7625800-7628400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:7625800-7631000	Enhancers	Psoas Muscle	Psoas
9	chr18:7626000-7628000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr18:7626000-7628000	Enhancers	Adipose Nuclei	Adipose
11	chr18:7626000-7628000	Enhancers	Fetal Heart	heart
12	chr18:7626000-7628200	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr18:7626400-7628000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:7626400-7628000	Enhancers	Stomach Smooth Muscle	stomach
15	chr18:7626400-7628000	Enhancers	NHDF-Ad	bronchial
16	chr18:7626400-7628200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr18:7626400-7628200	Enhancers	Lung	lung
18	chr18:7626600-7628000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:7626600-7628000	Enhancers	HUVEC	blood vessel
20	chr18:7626600-7628200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr18:7626600-7628200	Enhancers	Placenta	Placenta
22	chr18:7626800-7628200	Enhancers	HMEC	breast
23	chr18:7626800-7630400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr18:7627000-7628000	Enhancers	Muscle Satellite Cultured Cells	--
25	chr18:7627000-7628200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr18:7627200-7628200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr18:7627200-7636000	Weak transcription	Gastric	stomach
28	chr18:7627200-7637800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr18:7627400-7630200	Weak transcription	Fetal Lung	lung
30	chr18:7627400-7633000	Weak transcription	HSMM	muscle
31	chr18:7627600-7628200	Enhancers	A549	lung
32	chr18:7627600-7628400	Enhancers	HepG2	liver
33	chr18:7627600-7630000	Weak transcription	Small Intestine	intestine
34	chr18:7627600-7630200	Weak transcription	Ovary	ovary
35	chr18:7627600-7630200	Weak transcription	Pancreas	Pancrea
36	chr18:7627600-7636600	Weak transcription	Fetal Muscle Leg	muscle
37	chr18:7627800-7628800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr18:7627800-7629000	Weak transcription	Right Ventricle	heart
39	chr18:7627800-7630200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:7627800-7633000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr18:7627800-7637200	Weak transcription	NHLF	lung
42	chr18:7627800-7637400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links