Variant report

Variant	rs6896559
Chromosome Location	chr5:118678718-118678719
allele	C/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:
2	chr5:118666908..118671699-chr5:118672968..118679055,7	K562	blood:

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

Variant related genes	Relation type
ENSG00000145779	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10059175	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10477585	0.83[AFR][1000 genomes]
rs13155880	0.83[AFR][1000 genomes]
rs1396609	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17145265	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs250298	0.85[AFR][1000 genomes]
rs250299	0.85[AFR][1000 genomes]
rs250308	0.81[AFR][1000 genomes]
rs32653	0.83[AFR][1000 genomes]
rs32655	0.83[AFR][1000 genomes]
rs32657	0.83[AFR][1000 genomes]
rs32658	0.82[AFR][1000 genomes]
rs3797339	0.85[AFR][1000 genomes]
rs3797340	0.81[ASN][1000 genomes]
rs3797341	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3797343	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3813308	0.86[AFR][1000 genomes]
rs3920174	0.86[AFR][1000 genomes]
rs408095	0.81[AFR][1000 genomes]
rs67328001	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6863311	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6864305	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6869512	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6870253	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6876224	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6877025	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6882237	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6884061	0.90[ASN][1000 genomes]
rs6891084	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6896277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897359	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs73237292	0.90[ASN][1000 genomes]
rs73237297	0.86[ASN][1000 genomes]
rs7707470	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7731632	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs996934	0.83[AFR][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	chr5:118671800-118680000	Enhancers	Primary hematopoietic stem cells	blood
6	chr5:118673200-118679600	Enhancers	Fetal Heart	heart
7	chr5:118673200-118683600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:118673200-118683800	Weak transcription	Hela-S3	cervix
9	chr5:118673400-118683000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:118673600-118678800	Enhancers	Fetal Thymus	thymus
11	chr5:118673800-118683400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr5:118674000-118679800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:118674200-118681800	Weak transcription	Pancreas	Pancrea
14	chr5:118674200-118689000	Weak transcription	Esophagus	oesophagus
15	chr5:118674400-118681000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:118674400-118689000	Weak transcription	Gastric	stomach
17	chr5:118675600-118679000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr5:118675800-118678800	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr5:118675800-118678800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr5:118675800-118679000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:118676000-118678800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:118676000-118682400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:118676200-118681800	Weak transcription	Spleen	Spleen
24	chr5:118676600-118681800	Weak transcription	Right Atrium	heart
25	chr5:118676800-118679000	Enhancers	K562	blood
26	chr5:118676800-118679400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:118676800-118679400	Weak transcription	Placenta	Placenta
28	chr5:118676800-118680000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr5:118676800-118680200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:118676800-118681800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:118676800-118689000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr5:118676800-118691400	Weak transcription	Lung	lung
33	chr5:118677000-118678800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:118677000-118679000	Weak transcription	Stomach Mucosa	stomach
35	chr5:118677000-118679400	Weak transcription	Colonic Mucosa	Colon
36	chr5:118677000-118679600	Weak transcription	Dnd41	blood
37	chr5:118677000-118686000	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:118677200-118686800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr5:118677400-118678800	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr5:118677400-118680000	Enhancers	Fetal Stomach	stomach
41	chr5:118677400-118680200	Enhancers	Small Intestine	intestine
42	chr5:118677400-118680400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr5:118677400-118682600	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr5:118677600-118680200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:118677600-118680400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr5:118677600-118680400	Enhancers	NH-A	brain
47	chr5:118677800-118680200	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr5:118677800-118680400	Enhancers	Duodenum Mucosa	Duodenum
49	chr5:118677800-118681800	Enhancers	Primary T cells fromperipheralblood	blood
50	chr5:118677800-118681800	Enhancers	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links