Variant report

Variant	rs28343
Chromosome Location	chr5:14400123-14400124
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	chr5:14399431..14402316-chr5:14403363..14405249,2	K562	blood:
2	chr5:14393059..14395899-chr5:14399297..14401999,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11955578	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11957060	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957857	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13172149	0.91[EUR][1000 genomes]
rs13172877	0.91[EUR][1000 genomes]
rs13188746	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13189406	0.91[EUR][1000 genomes]
rs13356126	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs154151	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17304403	0.89[EUR][1000 genomes]
rs173947	1.00[ASN][1000 genomes]
rs185355	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs187190	0.87[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs187667	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247136	0.98[ASN][1000 genomes]
rs247137	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs256412	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256418	0.87[ASN][1000 genomes]
rs30606	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs30607	0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs30608	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs30609	0.88[ASN][1000 genomes]
rs30610	0.86[ASN][1000 genomes]
rs30611	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs30766	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30767	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30768	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30772	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs30785	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30786	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30787	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs30788	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30789	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs30790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30793	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs30794	1.00[JPT][hapmap]
rs30795	1.00[JPT][hapmap]
rs30799	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs30800	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30801	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35860741	0.90[EUR][1000 genomes]
rs36077682	0.89[EUR][1000 genomes]
rs378369	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs389729	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40572	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42206	1.00[ASN][1000 genomes]
rs42404	0.87[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs42555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434279	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4702029	0.90[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs71614085	0.86[EUR][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	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1018187	chr5:14385164-15127103	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28343	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14354600-14402400	Strong transcription	Liver	Liver
2	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
3	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:14366800-14403200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:14380400-14402800	Strong transcription	Primary B cells from peripheral blood	blood
7	chr5:14387200-14405800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:14388000-14402200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:14388200-14400200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:14388600-14402600	Strong transcription	Fetal Intestine Large	intestine
11	chr5:14388800-14407200	Weak transcription	Small Intestine	intestine
12	chr5:14392200-14402600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr5:14392200-14406600	Weak transcription	Primary T cells from cord blood	blood
14	chr5:14392400-14406000	Weak transcription	Fetal Heart	heart
15	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
16	chr5:14392600-14403600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:14393200-14402800	Strong transcription	Placenta	Placenta
18	chr5:14393400-14402400	Strong transcription	GM12878-XiMat	blood
19	chr5:14393400-14403200	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:14393600-14413600	Strong transcription	Primary B cells from cord blood	blood
21	chr5:14393800-14403000	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr5:14394200-14401800	Strong transcription	Fetal Brain Female	brain
23	chr5:14394400-14405200	Strong transcription	Fetal Intestine Small	intestine
24	chr5:14394600-14402200	Genic enhancers	NHLF	lung
25	chr5:14395200-14406600	Weak transcription	Fetal Kidney	kidney
26	chr5:14395600-14401000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:14395600-14402200	Genic enhancers	HSMM	muscle
28	chr5:14395800-14406000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:14395800-14406000	Weak transcription	Brain Substantia Nigra	brain
30	chr5:14396200-14402200	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr5:14396400-14401600	Genic enhancers	Osteobl	bone
32	chr5:14396600-14401400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:14397000-14400800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr5:14397000-14400800	Genic enhancers	HSMMtube	muscle
35	chr5:14397400-14402000	Weak transcription	Brain Anterior Caudate	brain
36	chr5:14397400-14402600	Weak transcription	Gastric	stomach
37	chr5:14397400-14402600	Weak transcription	Pancreas	Pancrea
38	chr5:14397400-14405400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:14397600-14400200	Weak transcription	Colon Smooth Muscle	Colon
40	chr5:14397600-14400200	Weak transcription	Right Ventricle	heart
41	chr5:14397600-14400800	Weak transcription	Fetal Lung	lung
42	chr5:14397600-14402400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr5:14397600-14405200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:14397600-14405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:14397600-14406200	Weak transcription	Brain Hippocampus Middle	brain
46	chr5:14397800-14401800	Genic enhancers	Fetal Stomach	stomach
47	chr5:14397800-14402600	Weak transcription	Brain Angular Gyrus	brain
48	chr5:14397800-14402800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr5:14398000-14400400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr5:14398000-14400600	Enhancers	HUVEC	blood vessel

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