Variant report

Variant	rs12504989
Chromosome Location	chr4:158918450-158918451
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:158918095..158920642-chr4:159082633..159084601,2	MCF-7	breast:
2	chr4:158914380..158920879-chr4:159079921..159084466,8	MCF-7	breast:
3	chr4:158916515..158919078-chr4:159032970..159035902,2	K562	blood:
4	chr4:158912006..158922011-chr4:159085009..159099282,46	MCF-7	breast:
5	chr4:158908850..158922778-chr4:159084957..159098830,43	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164125	Chromatin interaction
ENSG00000248429	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10517684	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10517688	0.81[CHB][hapmap]
rs10857307	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857308	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12498860	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501025	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12505752	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12505934	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12510436	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511578	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511957	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512064	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12643255	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12644342	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12650454	0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1375138	0.83[EUR][1000 genomes]
rs17036918	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036921	0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17037241	0.82[CHB][hapmap]
rs1839129	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1839130	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2245735	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs2594763	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2594769	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35146306	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35354204	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3934848	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4129400	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132016	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4132443	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4307005	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4460050	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4629502	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4637451	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4691449	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57156989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58762368	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335304	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335305	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335306	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335307	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335308	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335310	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335311	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335313	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335315	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62335339	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335341	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62335345	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62335346	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62335358	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62335359	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62336960	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62336961	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62336984	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6536298	1.00[JPT][hapmap]
rs6815131	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6827475	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72965897	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72967808	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72967836	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7384	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs964237	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs982239	0.95[AMR][1000 genomes];0.95[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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv881288	chr4:158891733-159028080	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:158913800-158918800	Enhancers	Fetal Intestine Small	intestine
2	chr4:158913800-158928200	Weak transcription	HSMM	muscle
3	chr4:158913800-158930000	Weak transcription	Right Atrium	heart
4	chr4:158914400-158923400	Weak transcription	Fetal Heart	heart
5	chr4:158915000-158924000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr4:158915800-158918800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr4:158916400-158918600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr4:158916400-158918800	Enhancers	HUVEC	blood vessel
9	chr4:158916400-158921400	Enhancers	HepG2	liver
10	chr4:158916400-158923000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr4:158917000-158918800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:158917200-158918800	Enhancers	Fetal Stomach	stomach
13	chr4:158917400-158918800	Enhancers	Fetal Lung	lung
14	chr4:158917400-158919000	Enhancers	Fetal Intestine Large	intestine
15	chr4:158917600-158918800	Enhancers	Colon Smooth Muscle	Colon
16	chr4:158917800-158918600	Weak transcription	Fetal Kidney	kidney
17	chr4:158917800-158919200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr4:158917800-158919800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:158917800-158922800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:158917800-158926400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr4:158918000-158918600	Weak transcription	Small Intestine	intestine
22	chr4:158918200-158923000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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