Variant report

Variant	rs1828178
Chromosome Location	chr5:90339314-90339315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:90318099..90320077-chr5:90338969..90341886,2	MCF-7	breast:
2	chr5:90339062..90340846-chr5:90677611..90679274,2	K562	blood:
3	chr5:90337875..90340059-chr5:90342694..90345036,3	K562	blood:
4	chr5:90338666..90340278-chr5:90352277..90353965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10038122	0.88[CEU][hapmap]
rs10942624	0.92[ASN][1000 genomes]
rs12109264	0.88[YRI][hapmap]
rs12186662	0.89[ASN][1000 genomes]
rs13179479	0.91[ASN][1000 genomes]
rs13180409	0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs16869403	1.00[YRI][hapmap]
rs1819073	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1819074	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1828177	1.00[CEU][hapmap];1.00[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]
rs1848483	0.87[CEU][hapmap]
rs1848485	0.88[CEU][hapmap]
rs1848486	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1848487	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1852734	0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1858070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1976565	0.88[CEU][hapmap]
rs2048217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367185	0.87[CEU][hapmap]
rs2367186	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2367274	0.95[ASN][1000 genomes]
rs2463775	0.99[ASN][1000 genomes]
rs2662278	0.95[ASN][1000 genomes]
rs2662279	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2662280	0.86[JPT][hapmap]
rs2662281	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2662282	0.91[ASN][1000 genomes]
rs2662283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2662284	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2697543	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs2697544	0.95[ASN][1000 genomes]
rs2697546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs28875340	0.87[ASN][1000 genomes]
rs2973444	0.83[YRI][hapmap]
rs2973448	0.84[YRI][hapmap]
rs4254936	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs4454077	0.95[ASN][1000 genomes]
rs4916839	0.88[CEU][hapmap]
rs6452928	0.88[CEU][hapmap]
rs6452930	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs6452934	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs6865615	0.95[CHB][hapmap]
rs6882081	0.81[ASN][1000 genomes]
rs689544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7706034	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs7719311	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs7723511	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs7733230	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs937920	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs998788	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv882369	chr5:90275825-90344149	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1024813	chr5:90321535-90870739	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	nsv537806	chr5:90321535-90870739	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90324600-90350400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:90335000-90340600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:90335000-90340800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:90335000-90344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:90335200-90344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90335400-90340600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:90337600-90339400	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr5:90337600-90339400	Enhancers	Fetal Intestine Large	intestine
9	chr5:90337600-90339600	Enhancers	Fetal Intestine Small	intestine
10	chr5:90337600-90339800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:90337600-90339800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:90337800-90339400	Enhancers	Primary hematopoietic stem cells	blood
13	chr5:90338000-90339400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:90338400-90339400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr5:90338400-90339400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr5:90338600-90339400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr5:90338600-90339400	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:90338600-90339400	Enhancers	HepG2	liver
19	chr5:90338800-90339400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:90339000-90339400	Enhancers	HUVEC	blood vessel
21	chr5:90339200-90339400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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