Variant report

Variant	rs6667703
Chromosome Location	chr1:58978601-58978602
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	chr1:58977602..58982967-chr1:59116778..59119321,4	MCF-7	breast:
2	chr1:58977617..58979668-chr1:58980963..58982878,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10789063	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10789067	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10889098	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[ASN][1000 genomes]
rs1114660	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207236	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11207237	0.88[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11207240	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1121422	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581395	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12030713	0.87[ASN][1000 genomes]
rs12088149	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12124662	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1388981	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1775002	0.82[ASN][1000 genomes]
rs232826	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs28529311	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs338224	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs338225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486463	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4912195	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912344	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6587818	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587819	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587828	0.87[ASN][1000 genomes]
rs659061	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6656025	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[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]
rs6667614	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6687324	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67639631	0.87[ASN][1000 genomes]
rs7517424	0.86[ASN][1000 genomes]
rs7520008	0.87[ASN][1000 genomes]
rs7536230	0.92[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544032	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7547036	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs7554278	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9660901	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv998092	chr1:58978327-59002319	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6667703	TACSTD2	cis	Thyroid	GTEx
rs6667703	DAB1///OMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58931200-59010800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:58933800-58984800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:58934800-58994000	Weak transcription	HSMM	muscle
4	chr1:58946200-58979600	Weak transcription	GM12878-XiMat	blood
5	chr1:58946400-58993800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:58953200-58986000	Weak transcription	Colonic Mucosa	Colon
7	chr1:58953600-58999200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:58955000-58986400	Weak transcription	Gastric	stomach
9	chr1:58955000-58988200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr1:58963800-58999000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:58964800-58986400	Weak transcription	K562	blood
12	chr1:58966600-59010600	Weak transcription	Placenta	Placenta
13	chr1:58967600-59010600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:58968200-58986400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:58968400-58984600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:58973800-58980600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:58974600-58987600	Weak transcription	Right Ventricle	heart
18	chr1:58974800-58978800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr1:58974800-58981800	Weak transcription	Brain Substantia Nigra	brain
20	chr1:58974800-58984600	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:58974800-58984600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:58974800-58984800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:58974800-58991600	Weak transcription	Esophagus	oesophagus
24	chr1:58974800-59005000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:58974800-59010800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:58974800-59011800	Weak transcription	Spleen	Spleen
27	chr1:58975000-59010600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:58975000-59010800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:58976600-58980600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:58976800-58980400	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:58977000-58979000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:58977000-58980200	Strong transcription	Liver	Liver
33	chr1:58977000-58980800	Strong transcription	Primary T cells from cord blood	blood
34	chr1:58977000-58980800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:58977000-58993000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:58977200-58979800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:58977200-58980200	Weak transcription	NHEK	skin
38	chr1:58977200-58980800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:58977200-58981800	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:58977200-58982400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr1:58977200-58984600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:58977200-58994000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:58977200-59005000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:58977200-59010800	Weak transcription	Brain Angular Gyrus	brain
45	chr1:58977200-59011400	Weak transcription	Ovary	ovary
46	chr1:58977400-58978800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr1:58977400-58978800	Weak transcription	Fetal Brain Female	brain
48	chr1:58977400-58980400	Weak transcription	Pancreas	Pancrea
49	chr1:58977400-58980800	Strong transcription	Primary B cells from cord blood	blood
50	chr1:58977400-58981800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links