Variant report

Variant	rs2984828
Chromosome Location	chr13:49051848-49051849
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10076	0.90[AMR][1000 genomes]
rs10467381	0.95[AMR][1000 genomes]
rs11840819	0.95[AMR][1000 genomes]
rs11842402	0.95[AMR][1000 genomes]
rs11842662	0.90[AMR][1000 genomes]
rs13378245	0.95[AMR][1000 genomes]
rs17071917	0.95[AMR][1000 genomes]
rs17071960	0.90[AMR][1000 genomes]
rs171989	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs174854	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs185587	0.92[EUR][1000 genomes]
rs198559	1.00[EUR][1000 genomes]
rs198565	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198566	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198567	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198572	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198573	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198581	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs198583	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198600	1.00[EUR][1000 genomes]
rs198601	1.00[EUR][1000 genomes]
rs198613	1.00[EUR][1000 genomes]
rs198616	1.00[EUR][1000 genomes]
rs198617	1.00[EUR][1000 genomes]
rs198618	1.00[EUR][1000 genomes]
rs198626	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs198628	1.00[EUR][1000 genomes]
rs198632	1.00[EUR][1000 genomes]
rs198636	1.00[EUR][1000 genomes]
rs2245534	0.92[EUR][1000 genomes]
rs2265777	0.92[EUR][1000 genomes]
rs2406932	0.92[EUR][1000 genomes]
rs2515668	0.92[EUR][1000 genomes]
rs2804082	1.00[EUR][1000 genomes]
rs2804084	1.00[EUR][1000 genomes]
rs2804085	1.00[EUR][1000 genomes]
rs2804086	1.00[EUR][1000 genomes]
rs2804087	1.00[EUR][1000 genomes]
rs2804088	1.00[EUR][1000 genomes]
rs2804089	1.00[EUR][1000 genomes]
rs2804091	0.92[EUR][1000 genomes]
rs2804092	0.92[EUR][1000 genomes]
rs2854352	0.92[EUR][1000 genomes]
rs2854356	0.92[EUR][1000 genomes]
rs2854363	1.00[EUR][1000 genomes]
rs2854364	1.00[EUR][1000 genomes]
rs2854365	0.92[EUR][1000 genomes]
rs3020646	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs411661	0.92[EUR][1000 genomes]
rs411862	1.00[EUR][1000 genomes]
rs4151590	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs416156	1.00[EUR][1000 genomes]
rs428431	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4587857	0.84[EUR][1000 genomes]
rs4625624	0.92[EUR][1000 genomes]
rs547747	1.00[EUR][1000 genomes]
rs61507973	0.92[EUR][1000 genomes]
rs7318012	0.92[EUR][1000 genomes]
rs7322110	0.95[AMR][1000 genomes]
rs7984270	0.95[AMR][1000 genomes]
rs7990103	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9285166	0.92[EUR][1000 genomes]
rs9316371	0.92[EUR][1000 genomes]
rs9316384	0.86[AMR][1000 genomes]
rs9316387	0.86[AMR][1000 genomes]
rs9316392	0.90[AMR][1000 genomes]
rs9316403	0.95[AMR][1000 genomes]
rs9332036	0.95[AMR][1000 genomes]
rs9332050	0.90[AMR][1000 genomes]
rs9332053	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9332066	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9332281	0.92[EUR][1000 genomes]
rs9562817	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]
rs9591167	0.95[AMR][1000 genomes]
rs9591170	0.95[AMR][1000 genomes]
rs9591171	0.90[AMR][1000 genomes]
rs9591174	0.95[AMR][1000 genomes]
rs9591175	0.95[AMR][1000 genomes]
rs9595894	1.00[EUR][1000 genomes]
rs9595909	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595910	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9595913	0.90[AMR][1000 genomes]
rs9595914	0.86[AMR][1000 genomes]
rs9595917	0.95[AMR][1000 genomes]
rs9595930	0.90[AMR][1000 genomes]
rs9595936	0.90[AMR][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	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49017400-49062200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:49018000-49062400	Weak transcription	Fetal Brain Male	brain
3	chr13:49020800-49062000	Weak transcription	Fetal Kidney	kidney
4	chr13:49021200-49058600	Weak transcription	Hela-S3	cervix
5	chr13:49023800-49061000	Weak transcription	Small Intestine	intestine
6	chr13:49023800-49073800	Weak transcription	NH-A	brain
7	chr13:49024000-49059000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr13:49025600-49056800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:49025600-49066200	Weak transcription	Psoas Muscle	Psoas
10	chr13:49028000-49071000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr13:49029200-49062000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:49029400-49052400	Weak transcription	K562	blood
13	chr13:49030600-49070600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr13:49031600-49055800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr13:49031600-49066200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr13:49031800-49052000	Weak transcription	HepG2	liver
17	chr13:49031800-49052600	Weak transcription	Placenta	Placenta
18	chr13:49031800-49059200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr13:49031800-49060200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:49031800-49060600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr13:49031800-49065400	Weak transcription	Brain Substantia Nigra	brain
22	chr13:49032000-49065600	Weak transcription	Brain Anterior Caudate	brain
23	chr13:49032000-49066200	Weak transcription	Colonic Mucosa	Colon
24	chr13:49032200-49053400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr13:49032200-49054000	Weak transcription	Aorta	Aorta
26	chr13:49032200-49056000	Weak transcription	Brain Germinal Matrix	brain
27	chr13:49032400-49052600	Weak transcription	NHLF	lung
28	chr13:49032400-49053000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr13:49032400-49062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:49032400-49066200	Weak transcription	Spleen	Spleen
31	chr13:49032400-49066600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:49032400-49066600	Weak transcription	Ovary	ovary
33	chr13:49032400-49067400	Weak transcription	Pancreas	Pancrea
34	chr13:49032400-49067600	Weak transcription	Gastric	stomach
35	chr13:49032600-49055000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr13:49032800-49066200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr13:49034400-49073800	Weak transcription	Esophagus	oesophagus
38	chr13:49035200-49073400	Weak transcription	Fetal Intestine Small	intestine
39	chr13:49035400-49052800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr13:49035600-49052000	Weak transcription	Liver	Liver
41	chr13:49035600-49052800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:49035600-49053400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr13:49035600-49065400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr13:49035600-49066000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr13:49035800-49052600	Weak transcription	Brain Angular Gyrus	brain
46	chr13:49035800-49056800	Weak transcription	Colon Smooth Muscle	Colon
47	chr13:49035800-49061800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:49035800-49066400	Weak transcription	NHEK	skin
49	chr13:49036600-49052600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:49038200-49053400	Weak transcription	Primary T helper cells fromperipheralblood	blood

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