Variant report

Variant	rs6858960
Chromosome Location	chr5:16542949-16542950
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:16527956..16530319-chr5:16542721..16545847,3	K562	blood:
2	chr5:16535725..16538550-chr5:16541937..16543644,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10053236	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1020952	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12109050	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1240647	0.82[ASN][1000 genomes]
rs1551936	1.00[CEU][hapmap];0.92[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]
rs162758	1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs162862	0.82[AFR][1000 genomes]
rs1991468	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991469	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991470	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991471	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1991472	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2019248	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2019260	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560830	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560831	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2560832	0.82[ASN][1000 genomes]
rs2617422	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617423	0.93[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617424	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617425	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2617426	0.93[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs31283	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs31288	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs334485	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs334486	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs334487	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs334490	0.83[ASN][1000 genomes]
rs334491	0.81[JPT][hapmap]
rs334492	0.82[ASN][1000 genomes]
rs425779	0.84[ASN][1000 genomes]
rs595358	0.83[ASN][1000 genomes]
rs899186	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs991891	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs994099	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16522400-16567400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr5:16533200-16543200	Enhancers	Fetal Heart	heart
3	chr5:16535400-16543400	Enhancers	Brain Cingulate Gyrus	brain
4	chr5:16535600-16546000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:16536800-16552800	Weak transcription	Thymus	Thymus
6	chr5:16538600-16546400	Weak transcription	Right Ventricle	heart
7	chr5:16539200-16554400	Weak transcription	Small Intestine	intestine
8	chr5:16539800-16545600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:16539800-16545600	Weak transcription	Esophagus	oesophagus
10	chr5:16539800-16545800	Weak transcription	Pancreas	Pancrea
11	chr5:16539800-16546400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr5:16539800-16548400	Weak transcription	Aorta	Aorta
13	chr5:16539800-16548400	Weak transcription	Gastric	stomach
14	chr5:16540400-16544000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr5:16540400-16545000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:16540600-16544600	Weak transcription	Fetal Intestine Small	intestine
17	chr5:16540800-16544200	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr5:16541000-16544200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:16541200-16543000	Weak transcription	NH-A	brain
20	chr5:16541200-16544200	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:16541200-16544200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr5:16541200-16544400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:16541200-16544600	Weak transcription	HSMMtube	muscle
24	chr5:16541200-16544800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr5:16541200-16544800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr5:16541200-16545000	Weak transcription	Brain Angular Gyrus	brain
27	chr5:16541200-16547000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:16541200-16547000	Weak transcription	HSMM	muscle
29	chr5:16541200-16548800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:16541200-16549600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr5:16541200-16552000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr5:16541400-16543000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr5:16541400-16543200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:16541400-16544800	Weak transcription	Brain Anterior Caudate	brain
35	chr5:16541400-16544800	Weak transcription	NHDF-Ad	bronchial
36	chr5:16541400-16544800	Weak transcription	NHEK	skin
37	chr5:16541400-16549800	Weak transcription	HMEC	breast
38	chr5:16541800-16543200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr5:16542000-16543000	Enhancers	Duodenum Mucosa	Duodenum
40	chr5:16542000-16543200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
41	chr5:16542000-16543400	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr5:16542200-16543000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr5:16542200-16543000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:16542200-16543200	Genic enhancers	Primary T cells from cord blood	blood
45	chr5:16542200-16543200	Enhancers	Fetal Intestine Large	intestine
46	chr5:16542200-16543200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr5:16542200-16543600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr5:16542200-16547800	Enhancers	Brain Substantia Nigra	brain
49	chr5:16542400-16543000	Enhancers	Psoas Muscle	Psoas
50	chr5:16542400-16543000	Weak transcription	Right Atrium	heart

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