Variant report

Variant	rs295946
Chromosome Location	chr5:58889057-58889058
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58879018..58880553-chr5:58887523..58890077,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10037874	0.93[ASN][1000 genomes]
rs159194	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs159196	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs159197	0.91[CHB][hapmap]
rs177077	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs294478	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs294479	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs294481	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs294482	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs294483	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs294484	0.90[CHB][hapmap]
rs294485	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs294486	0.92[CHB][hapmap];0.89[JPT][hapmap]
rs294492	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs294494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs294495	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs294496	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs294497	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs294498	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs294500	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295943	1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[ASN][1000 genomes]
rs295944	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295950	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295952	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295953	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295954	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295955	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs295956	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295959	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs295961	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs295963	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs295964	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295966	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs295967	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295968	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295970	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs295973	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs295979	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs295980	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs296406	0.87[CEU][hapmap]
rs298014	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298025	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs298027	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs298028	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs298029	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs298030	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs298032	0.92[CHB][hapmap];0.81[JPT][hapmap]
rs298033	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs298034	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs298038	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs298039	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298040	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs298043	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs298044	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298045	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298046	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs298048	1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs298049	0.91[ASN][1000 genomes]
rs298051	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs298052	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs37569	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs37571	0.92[CHB][hapmap];0.90[JPT][hapmap]
rs431381	0.88[EUR][1000 genomes];0.89[ASN][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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv881708	chr5:58869051-59093198	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58883800-58894200	Weak transcription	Aorta	Aorta
2	chr5:58884200-58892600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:58884200-58892600	Weak transcription	Osteobl	bone
4	chr5:58884200-58893800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:58884200-58894000	Weak transcription	Right Atrium	heart
6	chr5:58884200-58894200	Weak transcription	Liver	Liver
7	chr5:58884200-58902800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:58884400-58889400	Weak transcription	Brain Angular Gyrus	brain
9	chr5:58884600-58892200	Weak transcription	Small Intestine	intestine
10	chr5:58884600-58892600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:58884600-58893800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr5:58885000-58892200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:58885000-58894200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:58885200-58892400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr5:58885200-58892800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:58885400-58892200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:58885400-58892600	Weak transcription	HUVEC	blood vessel
18	chr5:58886800-58892800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:58887000-58892600	Weak transcription	HMEC	breast
20	chr5:58887000-58894200	Weak transcription	Fetal Intestine Large	intestine
21	chr5:58887000-58894200	Weak transcription	GM12878-XiMat	blood
22	chr5:58887400-58889200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:58887400-58894000	Weak transcription	Brain Substantia Nigra	brain
24	chr5:58888000-58892200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:58888200-58889400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:58888200-58892200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:58888200-58892600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:58888200-58892600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:58888200-58892800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:58888200-58893000	Weak transcription	Fetal Lung	lung
31	chr5:58888200-58894000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr5:58888200-58894200	Weak transcription	Psoas Muscle	Psoas
33	chr5:58888400-58889400	Weak transcription	Fetal Intestine Small	intestine
34	chr5:58888400-58891200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:58888400-58891200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:58888400-58891200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:58888400-58892200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:58888400-58892600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:58888400-58892600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:58888400-58892600	Weak transcription	HSMM	muscle
41	chr5:58888400-58893000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr5:58888400-58894000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:58888400-58894200	Weak transcription	Colon Smooth Muscle	Colon
44	chr5:58888800-58889200	Weak transcription	Hela-S3	cervix
45	chr5:58888800-58892400	Weak transcription	NHEK	skin
46	chr5:58889000-58890000	Enhancers	Stomach Mucosa	stomach
47	chr5:58889000-58890000	Flanking Active TSS	A549	lung

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