Variant report

Variant	rs6561497
Chromosome Location	chr13:49700334-49700335
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12872974	0.88[ASN][1000 genomes]
rs1359066	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs1407827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs1407829	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs1535922	0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs1928109	0.91[CHB][hapmap]
rs1937180	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs1937181	0.91[CHB][hapmap]
rs1983805	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs2021622	0.90[ASN][1000 genomes]
rs2026029	1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs2075610	0.89[GIH][hapmap]
rs2146748	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.94[ASN][1000 genomes]
rs2149498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs2181537	0.88[ASN][1000 genomes]
rs2181538	0.88[ASN][1000 genomes]
rs2181539	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2183095	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs2224742	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2407266	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs2897633	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs2897689	0.93[CHD][hapmap]
rs2987528	0.83[ASW][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];0.82[YRI][hapmap]
rs2987532	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.93[MKK][hapmap]
rs2994377	0.88[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs2994378	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs2994379	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.80[TSI][hapmap]
rs2994380	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs3012116	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs3012117	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs3012121	0.91[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs3012127	0.91[CHB][hapmap]
rs3012133	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs3012136	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs34360275	0.86[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs35018425	0.85[ASN][1000 genomes]
rs4142065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.90[ASN][1000 genomes]
rs4245350	0.82[ASN][1000 genomes]
rs4258502	0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs4530025	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs4942796	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs4942799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs4942800	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.88[ASN][1000 genomes]
rs6561493	0.88[ASN][1000 genomes]
rs6561496	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6561504	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7139819	0.81[ASN][1000 genomes]
rs716722	0.86[ASN][1000 genomes]
rs720627	0.91[CHB][hapmap];0.95[GIH][hapmap];0.80[MKK][hapmap]
rs728075	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7317908	0.85[ASN][1000 genomes]
rs7318871	0.88[ASN][1000 genomes]
rs7329291	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7331917	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7333097	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7333285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7338529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7983885	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs7986624	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7987258	0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7988168	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs7989175	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7990573	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7994368	0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs7994845	0.85[ASN][1000 genomes]
rs7994910	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs7995616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs7997118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs7998359	0.90[CHB][hapmap]
rs7999513	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap]
rs8248	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs9316426	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9316428	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs9316429	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9526518	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs9526520	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9526521	1.00[GIH][hapmap]
rs9526532	0.82[GIH][hapmap]
rs9535126	0.91[CHB][hapmap]
rs9535133	0.86[AFR][1000 genomes]
rs9535136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap]
rs9535140	0.88[ASN][1000 genomes]
rs9535141	0.85[ASN][1000 genomes]
rs9535145	0.91[CHB][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs9535146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.90[ASN][1000 genomes]
rs9535147	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs9535149	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9535154	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9535155	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs9535156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9535166	0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs9535167	0.94[ASW][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap]
rs9562866	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs9562870	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs9568143	0.83[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap]
rs9568150	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[TSI][hapmap];0.90[ASN][1000 genomes]
rs9568151	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9568154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9568169	0.89[GIH][hapmap];0.81[MKK][hapmap]
rs9596064	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs972297	0.80[CHD][hapmap];0.98[GIH][hapmap]

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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1035	chr13:49656225-49700371	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv1796840	chr13:49671215-49760666	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1052168	chr13:49691378-49743696	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6561497	HTR2A	cis	cerebellum	SCAN
rs6561497	RNASEH2B	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49685600-49705400	Weak transcription	K562	blood
2	chr13:49687600-49705800	Weak transcription	Small Intestine	intestine
3	chr13:49687600-49706200	Weak transcription	Fetal Heart	heart
4	chr13:49687600-49724200	Weak transcription	Esophagus	oesophagus
5	chr13:49687600-49789000	Weak transcription	Stomach Mucosa	stomach
6	chr13:49688000-49705000	Weak transcription	Right Ventricle	heart
7	chr13:49688200-49702200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:49689000-49711200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:49690200-49705200	Weak transcription	Brain Anterior Caudate	brain
10	chr13:49691400-49705400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:49691600-49702200	Weak transcription	Psoas Muscle	Psoas
12	chr13:49691800-49700800	Weak transcription	NHDF-Ad	bronchial
13	chr13:49691800-49705200	Weak transcription	HMEC	breast
14	chr13:49692000-49705200	Weak transcription	NHLF	lung
15	chr13:49692200-49701000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr13:49692600-49701000	Weak transcription	HUVEC	blood vessel
17	chr13:49692800-49705200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:49693400-49705200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:49693400-49705200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:49693400-49705200	Weak transcription	Aorta	Aorta
21	chr13:49693400-49706600	Weak transcription	A549	lung
22	chr13:49693600-49700600	Weak transcription	Fetal Muscle Leg	muscle
23	chr13:49693600-49700800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr13:49693600-49700800	Weak transcription	NHEK	skin
25	chr13:49693600-49701000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr13:49693600-49701000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:49693600-49701000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:49693600-49701200	Weak transcription	Primary B cells from cord blood	blood
29	chr13:49693600-49701400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr13:49693600-49704600	Weak transcription	Hela-S3	cervix
31	chr13:49693600-49705000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr13:49693600-49705000	Weak transcription	Fetal Intestine Small	intestine
33	chr13:49693600-49705000	Weak transcription	Fetal Stomach	stomach
34	chr13:49693600-49705000	Weak transcription	Gastric	stomach
35	chr13:49693600-49705200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr13:49693600-49705200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:49693600-49705200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:49693600-49705200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr13:49693600-49705200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr13:49693600-49705200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:49693600-49705200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr13:49693600-49705200	Weak transcription	Colonic Mucosa	Colon
43	chr13:49693600-49705200	Weak transcription	Lung	lung
44	chr13:49693600-49705200	Weak transcription	Ovary	ovary
45	chr13:49693600-49705200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr13:49693600-49705200	Weak transcription	Thymus	Thymus
47	chr13:49693600-49705200	Weak transcription	GM12878-XiMat	blood
48	chr13:49693600-49705400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:49693600-49705400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr13:49693600-49705400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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