Variant report

Variant	rs250298
Chromosome Location	chr5:118680047-118680048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118675434..118678874-chr5:118679948..118684456,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMXL1-8	chr5:118677271-118680524	NONHSAT103433

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10059175	1.00[YRI][hapmap]
rs10477585	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1112247	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13155880	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396609	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17145265	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs192225	0.82[CHB][hapmap]
rs250299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs250302	0.82[CHB][hapmap]
rs250303	0.81[CHB][hapmap]
rs250304	0.82[CHB][hapmap]
rs250308	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32653	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs32654	0.82[CHB][hapmap]
rs32655	0.98[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs32657	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs32658	0.88[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3797339	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797341	0.84[AFR][1000 genomes]
rs3797343	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs3813308	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3813309	0.81[CHB][hapmap]
rs3920174	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs408095	0.92[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs465091	0.80[JPT][hapmap]
rs4895369	0.82[CHB][hapmap]
rs4895372	0.85[JPT][hapmap]
rs67328001	0.83[AFR][1000 genomes]
rs6863311	0.86[AFR][1000 genomes]
rs6864305	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6869512	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6870253	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs6874848	0.80[CHB][hapmap]
rs6876224	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6877025	0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs6882237	0.86[AFR][1000 genomes]
rs6891084	0.84[AFR][1000 genomes]
rs6896277	0.85[AFR][1000 genomes]
rs6896553	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6896559	0.85[AFR][1000 genomes]
rs6897359	0.80[AFR][1000 genomes]
rs7707470	0.88[AFR][1000 genomes]
rs996934	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118680200	Enhancers	Thymus	Thymus
3	chr5:118671200-118681600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:118671200-118695400	Weak transcription	A549	lung
5	chr5:118673200-118683600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:118673200-118683800	Weak transcription	Hela-S3	cervix
7	chr5:118673400-118683000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:118673800-118683400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:118674200-118681800	Weak transcription	Pancreas	Pancrea
10	chr5:118674200-118689000	Weak transcription	Esophagus	oesophagus
11	chr5:118674400-118681000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:118674400-118689000	Weak transcription	Gastric	stomach
13	chr5:118676000-118682400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:118676200-118681800	Weak transcription	Spleen	Spleen
15	chr5:118676600-118681800	Weak transcription	Right Atrium	heart
16	chr5:118676800-118680200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:118676800-118681800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:118676800-118689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:118676800-118691400	Weak transcription	Lung	lung
20	chr5:118677000-118686000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr5:118677200-118686800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr5:118677400-118680200	Enhancers	Small Intestine	intestine
23	chr5:118677400-118680400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr5:118677400-118682600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr5:118677600-118680200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:118677600-118680400	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr5:118677600-118680400	Enhancers	NH-A	brain
28	chr5:118677800-118680200	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr5:118677800-118680400	Enhancers	Duodenum Mucosa	Duodenum
30	chr5:118677800-118681800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr5:118677800-118681800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr5:118677800-118683400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr5:118678000-118681600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:118678000-118681600	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr5:118678000-118681800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:118678000-118690600	Weak transcription	NHEK	skin
37	chr5:118678200-118680400	Enhancers	HSMM	muscle
38	chr5:118678200-118681200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr5:118678200-118681600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr5:118678200-118682200	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr5:118678200-118682600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr5:118678200-118682600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr5:118678200-118683400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:118678200-118684600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr5:118678400-118680200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr5:118678400-118680400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
47	chr5:118678400-118680800	Enhancers	HSMMtube	muscle
48	chr5:118678400-118682000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:118678600-118680200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr5:118678600-118680600	Genic enhancers	Primary B cells from peripheral blood	blood

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