Variant report

Variant	rs8006419
Chromosome Location	chr14:65500735-65500736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11620955	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11627531	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11628273	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12435835	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12587257	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4466998	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4586342	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4605081	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4899159	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7148590	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7155275	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7155454	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726668	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8012008	0.85[EUR][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	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8006419	SYNE2	cis	lymphoblastoid	seeQTL
rs8006419	ATP6V1D	cis	parietal	SCAN
rs8006419	CHURC1	cis	lymphoblastoid	seeQTL
rs8006419	CHURC1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65454800-65513800	Weak transcription	Stomach Mucosa	stomach
2	chr14:65459400-65508000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr14:65464400-65521200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:65470400-65539600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:65471200-65546200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr14:65473400-65501400	Weak transcription	NHLF	lung
7	chr14:65473800-65513800	Weak transcription	HMEC	breast
8	chr14:65475200-65509400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:65475800-65501600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:65480000-65507400	Weak transcription	Gastric	stomach
11	chr14:65480800-65507400	Weak transcription	Hela-S3	cervix
12	chr14:65483400-65528000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:65483600-65501400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:65487400-65505800	Weak transcription	HSMMtube	muscle
15	chr14:65488400-65502800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr14:65489000-65507600	Weak transcription	Lung	lung
17	chr14:65489200-65514000	Weak transcription	Small Intestine	intestine
18	chr14:65489600-65501400	Strong transcription	Fetal Muscle Leg	muscle
19	chr14:65491600-65502400	Strong transcription	Primary T cells from cord blood	blood
20	chr14:65491800-65501400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr14:65492800-65501000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr14:65492800-65505000	Strong transcription	Fetal Stomach	stomach
23	chr14:65493000-65501600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr14:65493000-65521400	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:65493200-65501800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr14:65493400-65508200	Weak transcription	Colonic Mucosa	Colon
27	chr14:65493600-65501800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:65494200-65501000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:65494200-65502200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr14:65494600-65507400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:65494600-65507600	Weak transcription	Right Ventricle	heart
32	chr14:65494800-65501600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr14:65494800-65507600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr14:65495000-65507200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:65496000-65507600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr14:65496200-65507400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr14:65496400-65502800	Strong transcription	Fetal Intestine Large	intestine
38	chr14:65496400-65513000	Strong transcription	Fetal Intestine Small	intestine
39	chr14:65496400-65515400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr14:65496800-65521200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr14:65497000-65501400	Weak transcription	K562	blood
42	chr14:65497200-65501400	Weak transcription	Brain Angular Gyrus	brain
43	chr14:65497200-65501400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr14:65497200-65502200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr14:65497200-65507400	Weak transcription	Dnd41	blood
46	chr14:65497400-65501400	Weak transcription	Spleen	Spleen
47	chr14:65497400-65501800	Weak transcription	Aorta	Aorta
48	chr14:65498400-65501000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:65498600-65502800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr14:65498800-65501200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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