Variant report

Variant	rs6561504
Chromosome Location	chr13:49749097-49749098
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs12872974	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1359066	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1407827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1407829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1535922	0.95[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1928109	0.83[CEU][hapmap];0.87[CHB][hapmap]
rs1937180	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1937181	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs1983805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2021622	0.81[EUR][1000 genomes]
rs2026029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2075610	0.82[AMR][1000 genomes]
rs2146748	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2147399	0.83[EUR][1000 genomes]
rs2149498	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2181537	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2181538	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2181539	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2183095	0.86[CEU][hapmap];0.91[CHB][hapmap]
rs2224742	0.86[ASN][1000 genomes]
rs2407266	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2897633	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2897689	0.90[CEU][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2987528	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2994377	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2994378	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2994379	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2994380	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs3012116	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs3012117	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs3012121	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs3012127	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs3012133	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs3012136	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs34360275	0.82[EUR][1000 genomes]
rs35018425	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142065	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs4245350	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4258502	0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs4530025	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4942796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs4942799	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs4942800	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6561493	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6561496	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6561497	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs67235936	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7139746	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7139819	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs716722	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728075	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs7317908	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318871	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7329291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs7333097	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs7333285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7983885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs7986624	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7987258	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap]
rs7988168	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7989175	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap]
rs7994368	0.83[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs7994845	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs7995616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap]
rs7996151	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7997118	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7998359	0.95[CEU][hapmap];0.86[CHB][hapmap]
rs7999513	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8248	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs9316426	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9316428	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9316429	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs9526518	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs9526520	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs9526525	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9526526	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535126	0.96[CEU][hapmap];0.87[CHB][hapmap]
rs9535136	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9535141	0.80[EUR][1000 genomes]
rs9535145	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs9535146	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9535147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs9535149	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9535154	0.95[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes]
rs9535155	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535166	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535167	0.95[CEU][hapmap];0.91[CHB][hapmap];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9562866	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9562870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568143	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9568150	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9568151	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9568154	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs972297	0.95[CEU][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49687600-49789000	Weak transcription	Stomach Mucosa	stomach
2	chr13:49721800-49751400	Weak transcription	NH-A	brain
3	chr13:49722800-49752800	Weak transcription	Psoas Muscle	Psoas
4	chr13:49724400-49765000	Weak transcription	A549	lung
5	chr13:49736400-49760000	Weak transcription	NHLF	lung
6	chr13:49737800-49788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:49738000-49777000	Weak transcription	Small Intestine	intestine
8	chr13:49738400-49750800	Weak transcription	Brain Angular Gyrus	brain
9	chr13:49738400-49754600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr13:49738400-49758000	Weak transcription	Fetal Heart	heart
11	chr13:49738400-49762000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr13:49738400-49785200	Strong transcription	Liver	Liver
13	chr13:49738600-49757200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:49738600-49761400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:49738600-49785000	Strong transcription	Dnd41	blood
16	chr13:49738800-49761800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:49739000-49750800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr13:49739000-49752200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:49739000-49761800	Weak transcription	Brain Hippocampus Middle	brain
20	chr13:49739000-49768200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr13:49739000-49774200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr13:49739200-49749400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:49739200-49751000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr13:49739200-49752400	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:49739200-49755600	Strong transcription	Primary T cells from cord blood	blood
26	chr13:49739600-49786400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:49739800-49755400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:49740000-49750400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:49740000-49752200	Weak transcription	Fetal Brain Male	brain
30	chr13:49740000-49752200	Weak transcription	Right Ventricle	heart
31	chr13:49740000-49757200	Weak transcription	HMEC	breast
32	chr13:49740000-49761600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr13:49740200-49751800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr13:49740200-49786000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:49740400-49751000	Weak transcription	Colonic Mucosa	Colon
36	chr13:49740400-49752400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr13:49740400-49756000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr13:49740400-49762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:49740400-49784800	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr13:49740600-49749800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:49740600-49752400	Weak transcription	Gastric	stomach
42	chr13:49740600-49752600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:49740600-49752600	Weak transcription	Lung	lung
44	chr13:49740600-49756600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:49740600-49768400	Strong transcription	Fetal Thymus	thymus
46	chr13:49740600-49769000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr13:49740600-49772800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr13:49740600-49786600	Strong transcription	Placenta	Placenta
49	chr13:49740800-49749600	Weak transcription	Fetal Brain Female	brain
50	chr13:49740800-49750800	Weak transcription	Ovary	ovary

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