Variant report

Variant	rs13374104
Chromosome Location	chr1:180405726-180405727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10914021	0.83[EUR][1000 genomes]
rs10914022	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs12407684	0.84[TSI][hapmap]
rs13373944	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13374665	0.82[ASW][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1416822	0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17300282	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17300340	0.95[GIH][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17300579	0.95[GIH][hapmap];0.92[TSI][hapmap]
rs17300600	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17300712	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17372281	0.90[GIH][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17372295	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17372362	0.95[GIH][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17372667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28816398	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4405110	0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4446932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4651065	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56759227	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57537558	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57882351	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58047798	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58677059	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59022209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59113753	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59829460	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60927564	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6425643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6672501	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6680668	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694896	0.91[EUR][1000 genomes]
rs6702245	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704001	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72712995	0.90[EUR][1000 genomes]
rs72713000	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72714804	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72714834	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72714847	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714855	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714856	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714861	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714864	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714866	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714870	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714877	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714879	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714887	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72714902	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72716607	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72716625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72716629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72716632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72720914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs74132851	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74135185	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7517775	0.82[ASW][hapmap];0.94[GIH][hapmap];0.92[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7525689	0.82[EUR][1000 genomes]
rs946636	0.90[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs961162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9650999	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv527918	chr1:180279710-180443808	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
6	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
7	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
8	nsv946528	chr1:180400421-180405841	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13374104	ACBD6	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180349400-180407000	Weak transcription	Esophagus	oesophagus
2	chr1:180356800-180406200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:180356800-180407000	Weak transcription	Aorta	Aorta
4	chr1:180361400-180407600	Weak transcription	HepG2	liver
5	chr1:180365200-180420600	Weak transcription	A549	lung
6	chr1:180376200-180407400	Weak transcription	NHLF	lung
7	chr1:180379000-180430800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:180379800-180406000	Weak transcription	Left Ventricle	heart
9	chr1:180380400-180408000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr1:180381200-180406400	Weak transcription	Fetal Stomach	stomach
11	chr1:180382400-180410800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:180382600-180406000	Weak transcription	Dnd41	blood
13	chr1:180382600-180406400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:180382600-180406600	Weak transcription	Hela-S3	cervix
15	chr1:180389600-180406000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:180389800-180410400	Weak transcription	Fetal Intestine Large	intestine
17	chr1:180391000-180409000	Weak transcription	Primary T cells from cord blood	blood
18	chr1:180391200-180410200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:180391800-180408000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:180392600-180446200	Weak transcription	K562	blood
21	chr1:180394400-180407000	Weak transcription	Psoas Muscle	Psoas
22	chr1:180394400-180407800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr1:180394600-180407000	Weak transcription	Brain Germinal Matrix	brain
24	chr1:180394800-180420200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:180398000-180408000	Weak transcription	Fetal Heart	heart
26	chr1:180399000-180420800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr1:180399400-180407000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:180399600-180420400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:180399600-180420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:180401400-180413800	Weak transcription	Small Intestine	intestine
31	chr1:180401400-180420200	Weak transcription	HSMM	muscle
32	chr1:180401400-180430400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:180401800-180408800	Weak transcription	Fetal Kidney	kidney
34	chr1:180401800-180410200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr1:180401800-180420800	Weak transcription	NHDF-Ad	bronchial
36	chr1:180402000-180406000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:180402400-180411400	Weak transcription	Spleen	Spleen
38	chr1:180402800-180409000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:180403200-180407000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:180403200-180408200	Weak transcription	Placenta	Placenta
41	chr1:180403200-180408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr1:180403400-180407000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:180403400-180408800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:180403400-180410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr1:180403400-180426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:180403400-180431200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:180403400-180448000	Weak transcription	HMEC	breast
48	chr1:180403600-180406000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:180403800-180406800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:180403800-180407400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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