Variant report

Variant	rs2804084
Chromosome Location	chr13:48916172-48916173
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11840676	0.92[EUR][1000 genomes]
rs171989	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs185587	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs198559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198565	1.00[EUR][1000 genomes]
rs198566	1.00[EUR][1000 genomes]
rs198567	1.00[EUR][1000 genomes]
rs198572	1.00[EUR][1000 genomes]
rs198573	1.00[EUR][1000 genomes]
rs198583	1.00[EUR][1000 genomes]
rs198587	1.00[EUR][1000 genomes]
rs198600	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198601	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198613	1.00[EUR][1000 genomes]
rs198616	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198617	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198626	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs198628	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198632	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198636	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245534	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2265777	0.92[EUR][1000 genomes]
rs2406932	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2515668	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804082	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804086	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804087	1.00[EUR][1000 genomes]
rs2804088	1.00[EUR][1000 genomes]
rs2804089	1.00[EUR][1000 genomes]
rs2804091	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804092	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854352	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854356	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2854363	1.00[EUR][1000 genomes]
rs2854364	1.00[EUR][1000 genomes]
rs2854365	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2984828	1.00[EUR][1000 genomes]
rs3020646	1.00[EUR][1000 genomes]
rs411661	0.92[EUR][1000 genomes]
rs411862	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4151590	0.92[EUR][1000 genomes]
rs416156	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs428431	1.00[EUR][1000 genomes]
rs4587857	0.84[EUR][1000 genomes]
rs4625624	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs547747	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61507973	0.92[EUR][1000 genomes]
rs7318012	0.92[EUR][1000 genomes]
rs7990103	1.00[EUR][1000 genomes]
rs8001351	0.92[EUR][1000 genomes]
rs9285166	0.92[EUR][1000 genomes]
rs9316371	0.92[EUR][1000 genomes]
rs9332053	0.82[EUR][1000 genomes]
rs9332066	0.82[EUR][1000 genomes]
rs9332248	0.92[EUR][1000 genomes]
rs9332281	0.92[EUR][1000 genomes]
rs9562817	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9591153	0.92[EUR][1000 genomes]
rs9591154	0.92[EUR][1000 genomes]
rs9591155	0.92[EUR][1000 genomes]
rs9591163	1.00[EUR][1000 genomes]
rs9595872	0.91[EUR][1000 genomes]
rs9595894	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595909	1.00[EUR][1000 genomes]
rs9595910	1.00[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	nsv1039312	chr13:48898950-48925357	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1038705	chr13:48899219-48922327	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1042504	chr13:48911264-48925357	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48880600-48924600	Weak transcription	Psoas Muscle	Psoas
2	chr13:48892600-48927800	Weak transcription	HUVEC	blood vessel
3	chr13:48894600-48919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr13:48895200-48916800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr13:48895200-48923600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr13:48895200-48924600	Weak transcription	HSMMtube	muscle
7	chr13:48895400-48924800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr13:48895800-48919600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr13:48895800-48920400	Weak transcription	Right Ventricle	heart
10	chr13:48895800-48926600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr13:48896000-48919800	Weak transcription	Primary T cells from cord blood	blood
12	chr13:48897000-48917000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:48903400-48924400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr13:48908400-48922200	Weak transcription	Liver	Liver
15	chr13:48908400-48944800	Weak transcription	Small Intestine	intestine
16	chr13:48908800-48917000	Weak transcription	NHDF-Ad	bronchial
17	chr13:48908800-48919200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:48908800-48919600	Weak transcription	HMEC	breast
19	chr13:48908800-48927600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:48909000-48923600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr13:48909000-48924400	Weak transcription	Osteobl	bone
22	chr13:48909000-48972200	Weak transcription	NHEK	skin
23	chr13:48909200-48916800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:48911600-48918000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr13:48911800-48919600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr13:48911800-48948400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr13:48912200-48968200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr13:48912800-48917600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:48913200-48919400	Weak transcription	Brain Anterior Caudate	brain
30	chr13:48913200-48924800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr13:48913400-48918000	Weak transcription	Fetal Muscle Leg	muscle
32	chr13:48913400-48923400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr13:48913400-48925800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:48913400-48944200	Weak transcription	Aorta	Aorta
35	chr13:48913600-48918400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr13:48913600-48918400	Weak transcription	Left Ventricle	heart
37	chr13:48913800-48919200	Weak transcription	Adipose Nuclei	Adipose
38	chr13:48913800-48923400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr13:48913800-48924800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:48913800-48924800	Weak transcription	Thymus	Thymus
41	chr13:48913800-48926200	Weak transcription	Gastric	stomach
42	chr13:48914000-48916800	Weak transcription	Primary B cells from cord blood	blood
43	chr13:48914000-48917400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:48914000-48918000	Weak transcription	Fetal Thymus	thymus
45	chr13:48914000-48918400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr13:48914000-48918400	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr13:48914000-48918400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr13:48914000-48920400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr13:48914000-48921200	Weak transcription	Fetal Intestine Small	intestine
50	chr13:48914000-48923400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links