Variant report

Variant	rs258290
Chromosome Location	chr5:14702375-14702376
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	chr5:14701491..14703497-chr5:14703505..14705062,2	K562	blood:
2	chr5:14680345..14681972-chr5:14701640..14703491,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154124	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs13189930	0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs149493	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149617	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs152788	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs153829	0.87[JPT][hapmap]
rs153830	0.87[JPT][hapmap]
rs1875513	0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.89[ASN][1000 genomes]
rs2455402	0.85[JPT][hapmap]
rs250439	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250440	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs258374	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs25945	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs25951	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs25952	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs25983	0.83[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs25986	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs25987	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs25988	0.84[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs25992	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs26307	0.93[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27356	0.87[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs27882	0.81[ASN][1000 genomes]
rs27911	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs28004	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs31919	0.82[ASN][1000 genomes]
rs31920	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs31921	0.81[ASN][1000 genomes]
rs31922	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs31923	0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs31925	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs31926	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs31928	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs31929	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs31930	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs31968	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3853119	0.84[ASN][1000 genomes]
rs3866215	0.82[CHB][hapmap];0.87[YRI][hapmap];0.88[ASN][1000 genomes]
rs40578	0.82[ASN][1000 genomes]
rs42358	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs42410	0.81[ASN][1000 genomes]
rs42681	0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs456180	0.93[JPT][hapmap]
rs466880	0.86[JPT][hapmap]
rs4702043	0.94[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6554856	0.87[JPT][hapmap]
rs6872954	0.94[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs745328	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs95492	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs258290	FAM105B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14674000-14712800	Strong transcription	Fetal Intestine Large	intestine
2	chr5:14676800-14705600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:14677600-14705600	Strong transcription	Dnd41	blood
4	chr5:14677800-14704000	Strong transcription	HepG2	liver
5	chr5:14678600-14704200	Strong transcription	Fetal Thymus	thymus
6	chr5:14684600-14726200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:14686800-14704200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:14687800-14702800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:14690800-14702600	Strong transcription	Primary B cells from cord blood	blood
10	chr5:14690800-14703000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:14690800-14704000	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:14690800-14706000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:14690800-14710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:14690800-14717200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:14691000-14711000	Weak transcription	Fetal Brain Male	brain
16	chr5:14691000-14711200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr5:14691000-14712800	Strong transcription	Hela-S3	cervix
18	chr5:14691000-14722200	Weak transcription	Stomach Mucosa	stomach
19	chr5:14691200-14720400	Weak transcription	Psoas Muscle	Psoas
20	chr5:14691600-14715000	Strong transcription	GM12878-XiMat	blood
21	chr5:14693400-14707600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr5:14694000-14717800	Weak transcription	Fetal Kidney	kidney
23	chr5:14694400-14706200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr5:14694600-14706800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:14696600-14702800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:14696600-14717800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr5:14696600-14727600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:14696800-14704200	Strong transcription	Thymus	Thymus
29	chr5:14696800-14711200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:14696800-14718600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:14697000-14712800	Strong transcription	Fetal Intestine Small	intestine
32	chr5:14697200-14704000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:14697400-14706000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:14698200-14702600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:14698400-14702800	Genic enhancers	Left Ventricle	heart
36	chr5:14698600-14706000	Weak transcription	HUVEC	blood vessel
37	chr5:14699000-14703800	Strong transcription	Lung	lung
38	chr5:14699000-14706400	Weak transcription	NH-A	brain
39	chr5:14699600-14705200	Weak transcription	Brain Germinal Matrix	brain
40	chr5:14699600-14705600	Weak transcription	Fetal Lung	lung
41	chr5:14699600-14712600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr5:14699800-14704800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:14699800-14705600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr5:14699800-14706400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr5:14699800-14706800	Weak transcription	Brain Angular Gyrus	brain
46	chr5:14700000-14702400	Enhancers	Right Ventricle	heart
47	chr5:14700000-14705400	Weak transcription	HSMMtube	muscle
48	chr5:14700000-14709400	Weak transcription	Ovary	ovary
49	chr5:14700000-14710000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
50	chr5:14700000-14711200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links