Variant report

Variant	rs1542413
Chromosome Location	chr6:70384098-70384099
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	chr6:70378773..70380366-chr6:70383381..70386352,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1031631	0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs11970363	0.85[YRI][hapmap]
rs12055543	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1457499	0.86[YRI][hapmap];0.86[AFR][1000 genomes]
rs1457500	0.86[AFR][1000 genomes]
rs1563608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1563610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1840940	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1840942	0.87[ASN][1000 genomes]
rs1902650	0.82[AFR][1000 genomes]
rs1993482	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2061310	0.85[AFR][1000 genomes]
rs2168712	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2345564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[ASN][1000 genomes]
rs2445957	0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs2445958	0.81[AFR][1000 genomes]
rs2445959	0.81[AFR][1000 genomes]
rs2445960	0.81[AFR][1000 genomes]
rs2445964	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2445973	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2445974	0.87[ASN][1000 genomes]
rs2445976	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2494776	0.98[ASN][1000 genomes]
rs2502543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2502564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2502597	0.84[CEU][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs3778241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3799112	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs3799113	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs3806960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs6455337	0.84[AFR][1000 genomes]
rs6455340	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6455342	0.85[ASN][1000 genomes]
rs6455344	0.85[EUR][1000 genomes]
rs6905645	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6935590	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7742015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7747908	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7749324	0.86[YRI][hapmap]
rs7749509	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7758405	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs7763213	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7774371	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs921973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9294848	0.84[AFR][1000 genomes]
rs930886	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9342766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9342768	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9346340	0.82[AFR][1000 genomes]
rs9346341	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9346342	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9354876	0.84[AFR][1000 genomes]
rs9354884	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9364046	0.84[AFR][1000 genomes]
rs9364050	0.81[AFR][1000 genomes]
rs960144	0.81[AFR][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	nsv886140	chr6:70354682-70728202	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:70377600-70392800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr6:70378400-70388000	Weak transcription	Esophagus	oesophagus
3	chr6:70378400-70392600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr6:70378600-70384200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr6:70378800-70385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:70378800-70386200	Weak transcription	Right Ventricle	heart
7	chr6:70378800-70388000	Weak transcription	Fetal Brain Female	brain
8	chr6:70378800-70388400	Weak transcription	Colonic Mucosa	Colon
9	chr6:70378800-70407400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:70378800-70409600	Weak transcription	Brain Substantia Nigra	brain
11	chr6:70378800-70416800	Weak transcription	Fetal Kidney	kidney
12	chr6:70378800-70430800	Weak transcription	Fetal Stomach	stomach
13	chr6:70378800-70430800	Weak transcription	Spleen	Spleen
14	chr6:70378800-70435200	Weak transcription	Psoas Muscle	Psoas
15	chr6:70379000-70428400	Weak transcription	Ovary	ovary
16	chr6:70379000-70435400	Weak transcription	Fetal Brain Male	brain
17	chr6:70379200-70390200	Weak transcription	HSMM	muscle
18	chr6:70379600-70431000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:70380000-70387200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:70380000-70387400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr6:70380000-70387600	Strong transcription	Liver	Liver
22	chr6:70380000-70390600	Weak transcription	Thymus	Thymus
23	chr6:70380000-70390800	Weak transcription	Pancreas	Pancrea
24	chr6:70380200-70384600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr6:70380200-70387400	Strong transcription	Fetal Thymus	thymus
26	chr6:70380200-70391000	Strong transcription	Primary B cells from cord blood	blood
27	chr6:70380200-70392800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:70380200-70407600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr6:70380400-70385400	Weak transcription	Gastric	stomach
30	chr6:70380400-70390800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:70380400-70430600	Weak transcription	Fetal Intestine Small	intestine
32	chr6:70380600-70386600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:70380600-70455600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:70380800-70388000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:70380800-70402800	Weak transcription	NHDF-Ad	bronchial
36	chr6:70380800-70467800	Weak transcription	K562	blood
37	chr6:70381000-70384200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:70381200-70384400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:70381200-70384600	Strong transcription	Primary T cells from cord blood	blood
40	chr6:70381200-70385600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr6:70381200-70387000	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr6:70381200-70388600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:70381400-70384400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:70381400-70387200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr6:70381400-70387400	Strong transcription	Adipose Nuclei	Adipose
46	chr6:70381400-70387600	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:70381600-70384400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:70381600-70385000	Strong transcription	Fetal Intestine Large	intestine
49	chr6:70381600-70385000	Strong transcription	Left Ventricle	heart
50	chr6:70381600-70385000	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links