Variant report

Variant	rs2804089
Chromosome Location	chr13:48973295-48973296
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs11840676	0.92[EUR][1000 genomes]
rs171989	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs171991	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs174858	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs185587	0.92[EUR][1000 genomes]
rs198559	1.00[EUR][1000 genomes]
rs198560	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs198565	1.00[EUR][1000 genomes]
rs198566	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198567	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198572	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198573	1.00[EUR][1000 genomes]
rs198580	0.81[AFR][1000 genomes]
rs198583	1.00[EUR][1000 genomes]
rs198587	1.00[EUR][1000 genomes]
rs198589	0.80[AFR][1000 genomes]
rs198600	1.00[EUR][1000 genomes]
rs198601	1.00[EUR][1000 genomes]
rs198613	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs198616	1.00[EUR][1000 genomes]
rs198617	1.00[EUR][1000 genomes]
rs198618	1.00[EUR][1000 genomes]
rs198626	0.82[AMR][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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2804088	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];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	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854365	0.92[EUR][1000 genomes]
rs2984828	1.00[EUR][1000 genomes]
rs3020646	1.00[EUR][1000 genomes]
rs411661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs411862	1.00[EUR][1000 genomes]
rs4151590	0.92[EUR][1000 genomes]
rs416156	1.00[EUR][1000 genomes]
rs428431	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs443211	0.83[AFR][1000 genomes]
rs449151	0.81[AFR][1000 genomes]
rs4587857	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];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]
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	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	1.00[EUR][1000 genomes]
rs9595909	1.00[EUR][1000 genomes]
rs9595910	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803998	chr13:48966078-48986320	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1050786	chr13:48971510-48987032	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
2	chr13:48920200-48974400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:48925200-48974800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr13:48925400-48976400	Weak transcription	Ovary	ovary
5	chr13:48933400-48974000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
7	chr13:48936000-48974600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
9	chr13:48944000-48974400	Weak transcription	Brain Anterior Caudate	brain
10	chr13:48944200-48973800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
12	chr13:48945400-48974400	Weak transcription	Small Intestine	intestine
13	chr13:48954800-48975000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr13:48956000-48974000	Weak transcription	Colon Smooth Muscle	Colon
15	chr13:48956200-48976600	Weak transcription	Liver	Liver
16	chr13:48964000-48974400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr13:48965200-48974400	Weak transcription	Fetal Heart	heart
18	chr13:48966400-48974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr13:48966400-48986000	Weak transcription	Lung	lung
20	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
21	chr13:48967600-48974600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr13:48968200-48976400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr13:48968400-48976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr13:48968800-48974200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr13:48968800-48974800	Weak transcription	Primary T cells from cord blood	blood
26	chr13:48968800-48976400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr13:48968800-48977800	Weak transcription	Spleen	Spleen
28	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach
29	chr13:48969000-48974400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr13:48969000-48984200	Weak transcription	Fetal Intestine Large	intestine
31	chr13:48969000-48984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:48969200-48974000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr13:48969200-48974400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr13:48969200-48975000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr13:48969200-48975000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr13:48969200-48976400	Weak transcription	Fetal Thymus	thymus
37	chr13:48969200-48976600	Weak transcription	Left Ventricle	heart
38	chr13:48969200-48976600	Weak transcription	Thymus	Thymus
39	chr13:48969200-48978000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:48969200-48978000	Weak transcription	Esophagus	oesophagus
41	chr13:48969200-48984200	Weak transcription	Fetal Stomach	stomach
42	chr13:48969200-48984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr13:48970000-48974800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr13:48970200-48974000	Weak transcription	HSMM	muscle
45	chr13:48970200-48974400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr13:48970200-48977600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr13:48970400-48974000	Weak transcription	Primary B cells from cord blood	blood
48	chr13:48970400-48976400	Weak transcription	Fetal Muscle Leg	muscle
49	chr13:48970600-48974000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr13:48970600-48974000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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