Variant report

Variant	rs4379670
Chromosome Location	chr1:154439865-154439866
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154435097..154437712-chr1:154439386..154441987,2	MCF-7	breast:
2	chr1:154299377..154301851-chr1:154439131..154442124,2	MCF-7	breast:
3	chr1:154377367..154378131-chr1:154439226..154439911,3	MCF-7	breast:
4	chr1:154377223..154380396-chr1:154438444..154440442,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction
ENSG00000228013	Chromatin interaction
ENSG00000143515	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10047079	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10752641	0.86[ASN][1000 genomes]
rs10908839	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11490956	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12403537	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405637	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12406822	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12408461	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2229238	0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35699331	0.86[ASN][1000 genomes]
rs3811448	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3811449	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4072391	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41269915	0.88[EUR][1000 genomes]
rs41308419	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41313910	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4240872	0.86[ASN][1000 genomes]
rs4341355	0.86[ASN][1000 genomes]
rs4390168	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4509570	0.86[ASN][1000 genomes]
rs4633282	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4639752	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57783436	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58348886	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58710275	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58881140	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59084843	0.89[EUR][1000 genomes]
rs59239860	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59741504	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59838898	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60092776	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60255122	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60368585	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60498985	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60760897	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60931472	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61275241	0.87[EUR][1000 genomes]
rs61403567	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61559765	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61698846	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6427672	0.81[ASN][1000 genomes]
rs6669229	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672087	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6674171	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6675472	0.81[EUR][1000 genomes]
rs6681207	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6687597	0.86[ASN][1000 genomes]
rs6698040	0.86[ASN][1000 genomes]
rs72999415	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72999419	0.88[EUR][1000 genomes]
rs72999422	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73018293	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73020232	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73020234	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73020246	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73023331	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73023339	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73023346	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73023348	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73023349	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7514452	0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7526293	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7537291	0.86[ASN][1000 genomes]
rs7537316	0.86[ASN][1000 genomes]
rs7546068	0.86[ASN][1000 genomes]
rs7546552	0.86[ASN][1000 genomes]
rs7546555	0.86[ASN][1000 genomes]
rs7551873	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7556449	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4379670	TDRD10	cis	lung	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
2	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
3	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
4	chr1:154426800-154442200	Weak transcription	HepG2	liver
5	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:154427800-154464800	Weak transcription	Ovary	ovary
7	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:154431600-154441400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:154432000-154442000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:154435200-154441000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:154435600-154440000	Enhancers	Primary hematopoietic stem cells	blood
12	chr1:154435600-154441400	Enhancers	Fetal Thymus	thymus
13	chr1:154436200-154440800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:154436200-154441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:154436200-154441200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:154436400-154441800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:154436400-154446400	Weak transcription	NHEK	skin
18	chr1:154436400-154446600	Weak transcription	HMEC	breast
19	chr1:154436600-154440600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:154436600-154441000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:154436600-154441200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:154436600-154441200	Weak transcription	Fetal Brain Male	brain
23	chr1:154436600-154441600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:154436600-154441600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:154436600-154446800	Weak transcription	NHDF-Ad	bronchial
26	chr1:154436600-154450600	Weak transcription	HUVEC	blood vessel
27	chr1:154437200-154441600	Strong transcription	Lung	lung
28	chr1:154437400-154442000	Weak transcription	Colonic Mucosa	Colon
29	chr1:154437800-154440200	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:154437800-154440400	Enhancers	GM12878-XiMat	blood
31	chr1:154437800-154442800	Enhancers	Brain Hippocampus Middle	brain
32	chr1:154438000-154442600	Weak transcription	Fetal Stomach	stomach
33	chr1:154438200-154441400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:154438200-154442200	Weak transcription	Stomach Mucosa	stomach
35	chr1:154438400-154440000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:154438400-154440000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:154438400-154441000	Weak transcription	Right Ventricle	heart
38	chr1:154438400-154441000	Weak transcription	Spleen	Spleen
39	chr1:154438400-154445800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:154438400-154446000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:154438400-154457800	Weak transcription	Pancreas	Pancrea
42	chr1:154438400-154458400	Weak transcription	Gastric	stomach
43	chr1:154438400-154463400	Weak transcription	Esophagus	oesophagus
44	chr1:154438600-154440000	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr1:154438600-154440200	Strong transcription	Liver	Liver
46	chr1:154438600-154440600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:154438600-154440800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:154438600-154441200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:154438600-154442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr1:154438600-154446800	Weak transcription	NHLF	lung

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