Variant report

Variant	rs389729
Chromosome Location	chr5:14405895-14405896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr5:14405352-14407509	IMR90	lung:	n/a	chr5:14405924-14405939
2	JUND	chr5:14405705-14408375	SK-N-SH	brain:	n/a	chr5:14407724-14407738 chr5:14405848-14405860
3	TCF12	chr5:14405496-14407266	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr5:14405233-14406108	HUVEC	blood vessel:	n/a	n/a
5	PBX3	chr5:14405845-14407249	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr5:14405816-14408578	U87	brain:	n/a	n/a
7	GATA3	chr5:14405845-14407298	SK-N-SH	brain:	n/a	chr5:14406261-14406282 chr5:14406268-14406275 chr5:14406266-14406276 chr5:14406268-14406275 chr5:14406268-14406275
8	MAZ	chr5:14405448-14407773	IMR90	lung:	n/a	chr5:14406138-14406148
9	EP300	chr5:14405803-14407243	SK-N-SH	brain:	n/a	n/a
10	RAD21	chr5:14405067-14405993	SK-N-SH	brain:	n/a	chr5:14405491-14405505
11	CTCF	chr5:14405199-14406264	SK-N-SH	brain:	n/a	chr5:14405582-14405598 chr5:14405576-14405597 chr5:14405581-14405599
12	POLR2A	chr5:14405822-14408518	U87	brain:	n/a	n/a

Variant related genes	Relation type
TRIO	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11955578	0.94[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs11957060	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11957857	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs13356126	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.96[ASN][1000 genomes]
rs154151	0.81[AMR][1000 genomes]
rs173947	0.96[ASN][1000 genomes]
rs185355	0.81[AMR][1000 genomes]
rs187190	1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs187667	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247136	0.94[ASN][1000 genomes]
rs247137	0.81[AMR][1000 genomes]
rs256412	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs256418	0.83[ASN][1000 genomes]
rs28343	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30606	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30607	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs30608	1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs30609	0.92[ASN][1000 genomes]
rs30610	0.90[ASN][1000 genomes]
rs30611	1.00[ASW][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs30766	0.85[AMR][1000 genomes]
rs30767	0.85[AMR][1000 genomes]
rs30768	0.88[AMR][1000 genomes]
rs30772	0.81[AMR][1000 genomes]
rs30773	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30774	0.85[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30785	0.81[AMR][1000 genomes]
rs30786	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs30787	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs30788	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs30789	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs30790	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs30791	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs30793	0.85[AMR][1000 genomes]
rs30794	1.00[JPT][hapmap]
rs30795	1.00[JPT][hapmap]
rs30799	0.81[EUR][1000 genomes]
rs30800	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30801	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs378369	0.94[CEU][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs382403	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs397319	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40278	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40572	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs42206	0.96[ASN][1000 genomes]
rs42404	1.00[ASW][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs42555	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs42556	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs434279	0.81[AMR][1000 genomes]
rs4702029	0.85[CEU][hapmap];0.84[TSI][hapmap]

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
rs389729	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
2	chr5:14363800-14430600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr5:14363800-14430600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:14388800-14407200	Weak transcription	Small Intestine	intestine
5	chr5:14392200-14406600	Weak transcription	Primary T cells from cord blood	blood
6	chr5:14392400-14406000	Weak transcription	Fetal Heart	heart
7	chr5:14392400-14426800	Weak transcription	Psoas Muscle	Psoas
8	chr5:14393600-14413600	Strong transcription	Primary B cells from cord blood	blood
9	chr5:14395200-14406600	Weak transcription	Fetal Kidney	kidney
10	chr5:14395800-14406000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:14395800-14406000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:14397600-14406200	Weak transcription	Brain Hippocampus Middle	brain
13	chr5:14398200-14406000	Weak transcription	Thymus	Thymus
14	chr5:14398400-14406000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:14398600-14406000	Weak transcription	Esophagus	oesophagus
16	chr5:14398800-14406200	Weak transcription	Aorta	Aorta
17	chr5:14399000-14419800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:14399600-14416400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr5:14400200-14413400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:14400400-14406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr5:14400600-14415000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:14400800-14408600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr5:14400800-14416000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:14401000-14406600	Weak transcription	Left Ventricle	heart
25	chr5:14401200-14406200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:14401200-14407400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:14401400-14406200	Weak transcription	Colon Smooth Muscle	Colon
28	chr5:14401400-14406600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:14401600-14406000	Weak transcription	Colonic Mucosa	Colon
30	chr5:14401600-14407400	Strong transcription	Fetal Muscle Leg	muscle
31	chr5:14401800-14407200	Weak transcription	Fetal Brain Male	brain
32	chr5:14402000-14406000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr5:14402000-14406000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr5:14402600-14406400	Weak transcription	Hela-S3	cervix
35	chr5:14402600-14407200	Strong transcription	Fetal Stomach	stomach
36	chr5:14402600-14407600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:14403200-14406000	Weak transcription	Fetal Lung	lung
38	chr5:14403200-14410000	Weak transcription	Brain Angular Gyrus	brain
39	chr5:14404000-14409400	Genic enhancers	HSMM	muscle
40	chr5:14404000-14420600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:14404200-14406000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:14404200-14412600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr5:14404400-14415000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr5:14404400-14428600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:14404600-14407000	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr5:14404600-14409400	Genic enhancers	Osteobl	bone
47	chr5:14404600-14414800	Strong transcription	Brain Germinal Matrix	brain
48	chr5:14404600-14427600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr5:14404800-14406000	Strong transcription	Ovary	ovary
50	chr5:14404800-14406000	Strong transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links