Variant report

Variant	rs7078586
Chromosome Location	chr10:52394773-52394774
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52154324..52156059-chr10:52394056..52396919,2	K562	blood:
2	chr10:52389046..52395992-chr10:52408718..52416095,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASAH2B-2	chr10:52389337-52401211	ENSG00000226200.2

Variant related genes	Relation type
ENSG00000231345	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10826032	1.00[ASN][1000 genomes]
rs10826101	1.00[ASN][1000 genomes]
rs11005595	1.00[ASN][1000 genomes]
rs11005708	1.00[ASN][1000 genomes]
rs11005872	1.00[ASN][1000 genomes]
rs11005877	1.00[ASN][1000 genomes]
rs11005882	1.00[ASN][1000 genomes]
rs11005952	1.00[ASN][1000 genomes]
rs11005956	1.00[ASN][1000 genomes]
rs11006012	1.00[ASN][1000 genomes]
rs11516712	1.00[ASN][1000 genomes]
rs11591645	1.00[ASN][1000 genomes]
rs11595661	1.00[ASN][1000 genomes]
rs1203383	0.86[TSI][hapmap]
rs1203391	0.86[TSI][hapmap]
rs12354779	1.00[ASN][1000 genomes]
rs13376734	0.93[CEU][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs2208037	0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2860490	0.83[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs2983348	0.86[TSI][hapmap]
rs2983352	0.89[TSI][hapmap]
rs2983362	0.82[GIH][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap]
rs2983363	0.83[GIH][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs2983365	0.85[EUR][1000 genomes]
rs3001853	0.93[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs3001855	1.00[CEU][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3001856	0.97[EUR][1000 genomes]
rs3001857	0.94[EUR][1000 genomes]
rs3001858	0.88[EUR][1000 genomes]
rs3001859	0.92[EUR][1000 genomes]
rs3001860	0.83[EUR][1000 genomes]
rs3001861	0.92[EUR][1000 genomes]
rs3001864	0.91[EUR][1000 genomes]
rs3001865	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs3001866	0.90[EUR][1000 genomes]
rs3001867	0.91[EUR][1000 genomes]
rs3001884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.83[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs3011717	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3011718	0.87[EUR][1000 genomes]
rs3011728	0.92[EUR][1000 genomes]
rs3011729	0.86[EUR][1000 genomes]
rs3011730	0.86[EUR][1000 genomes]
rs3011731	0.86[EUR][1000 genomes]
rs3011738	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3011739	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs3011748	0.82[EUR][1000 genomes]
rs3011752	0.88[EUR][1000 genomes]
rs56153288	0.98[EUR][1000 genomes]
rs56266445	0.98[EUR][1000 genomes]
rs57025029	0.94[EUR][1000 genomes]
rs57959812	1.00[ASN][1000 genomes]
rs67094247	0.96[EUR][1000 genomes]
rs7067608	0.98[EUR][1000 genomes]
rs7071001	1.00[ASN][1000 genomes]
rs7074349	0.96[EUR][1000 genomes]
rs7077555	0.93[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7078940	1.00[ASN][1000 genomes]
rs7082728	1.00[ASN][1000 genomes]
rs7091881	1.00[ASN][1000 genomes]
rs7096920	0.93[CEU][hapmap];0.96[EUR][1000 genomes]
rs7096968	1.00[ASN][1000 genomes]
rs7099535	1.00[ASN][1000 genomes]
rs72787008	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72803755	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74132723	1.00[ASN][1000 genomes]
rs7897345	0.93[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs7904446	0.96[EUR][1000 genomes]
rs7908093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs910819	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv469522	chr10:52276564-52447589	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv482564	chr10:52276564-52447589	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7078586	C20orf103	trans	lymphoblastoid	seeQTL
rs7078586	CSTF2T	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52385600-52395200	Weak transcription	Esophagus	oesophagus
2	chr10:52385800-52394800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr10:52385800-52395000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:52385800-52396000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:52385800-52396800	Weak transcription	Fetal Brain Male	brain
6	chr10:52385800-52397000	Weak transcription	Psoas Muscle	Psoas
7	chr10:52385800-52397000	Weak transcription	Small Intestine	intestine
8	chr10:52386000-52394800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:52386000-52394800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:52386000-52394800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr10:52386000-52394800	Weak transcription	HSMM	muscle
12	chr10:52386000-52395000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr10:52386000-52395200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr10:52386000-52395800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr10:52386000-52396000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr10:52386000-52397000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:52386000-52400400	Weak transcription	Fetal Lung	lung
18	chr10:52386200-52396200	Weak transcription	Primary B cells from cord blood	blood
19	chr10:52386200-52396200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr10:52389600-52396000	Weak transcription	GM12878-XiMat	blood
21	chr10:52390200-52397000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:52390200-52397000	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:52390800-52396600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr10:52393600-52394800	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr10:52393600-52395000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr10:52393600-52395400	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr10:52393800-52395000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr10:52393800-52395200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr10:52394000-52395000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr10:52394000-52395000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr10:52394000-52395400	Weak transcription	Primary T cells from cord blood	blood
32	chr10:52394600-52395600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr10:52394600-52396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr10:52394600-52397000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr10:52394600-52397000	Enhancers	Osteobl	bone
36	chr10:52394600-52397200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr10:52394600-52397400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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