Variant report

Variant	rs477842
Chromosome Location	chr5:177888014-177888015
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177887745..177890184-chr5:177903224..177905118,2	K562	blood:
2	chr5:177885956..177889656-chr5:177894667..177897889,3	MCF-7	breast:
3	chr5:177865902..177866648-chr5:177887888..177888885,2	K562	blood:
4	chr5:177706996..177707580-chr5:177887844..177888573,2	K562	blood:
5	chr5:177887805..177889193-chr5:178016576..178017370,3	MCF-7	breast:
6	chr5:177887719..177888721-chr5:177977307..177978270,3	MCF-7	breast:
7	chr5:177881991..177885625-chr5:177886030..177888202,3	MCF-7	breast:
8	chr5:177882178..177883994-chr5:177886180..177888676,2	K562	blood:

No data

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10051479	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10053433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078495	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12516264	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12652427	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12657817	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13159176	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs13179262	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13179385	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1498617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1846371	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2133281	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs2546626	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4288132	0.91[ASN][1000 genomes]
rs4329031	0.95[ASN][1000 genomes]
rs6601239	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs67405022	0.97[ASN][1000 genomes]
rs678011	0.98[ASN][1000 genomes]
rs6867956	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6881003	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7725796	0.82[JPT][hapmap];0.97[ASN][1000 genomes]
rs7726272	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9332465	0.93[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv427739	chr5:177766033-177966666	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv883210	chr5:177771925-177980792	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv883213	chr5:177811754-177947771	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv462570	chr5:177860454-178010145	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv600423	chr5:177860454-178010145	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1029822	chr5:177872333-177931889	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv1033039	chr5:177873974-177926244	Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv537971	chr5:177873974-177926244	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv883214	chr5:177876309-178047217	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1030915	chr5:177880081-177934927	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs477842	GPRIN1	cis	parietal	SCAN
rs477842	CLK4	cis	cerebellum	SCAN
rs477842	NSD1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177874600-177888200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:177877600-177894200	Weak transcription	Spleen	Spleen
3	chr5:177877800-177895400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:177887200-177888600	Enhancers	Placenta	Placenta
5	chr5:177887200-177889200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:177887200-177889400	Enhancers	Fetal Heart	heart
7	chr5:177887200-177896600	Enhancers	Fetal Stomach	stomach
8	chr5:177887400-177889000	Enhancers	Fetal Thymus	thymus
9	chr5:177887400-177889600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr5:177887600-177888200	Enhancers	Colon Smooth Muscle	Colon
11	chr5:177887600-177888400	Enhancers	Fetal Lung	lung
12	chr5:177887600-177888600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr5:177887600-177888600	Enhancers	Right Ventricle	heart
14	chr5:177887600-177888800	Enhancers	Stomach Smooth Muscle	stomach
15	chr5:177887600-177889200	Enhancers	Fetal Muscle Leg	muscle
16	chr5:177887600-177890000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:177887600-177890600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr5:177887800-177888400	Enhancers	Aorta	Aorta
19	chr5:177887800-177888600	Enhancers	Right Atrium	heart
20	chr5:177887800-177888600	Enhancers	Thymus	Thymus
21	chr5:177887800-177897600	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr5:177888000-177888400	Enhancers	Pancreas	Pancrea
23	chr5:177888000-177888600	Enhancers	Liver	Liver
24	chr5:177888000-177888600	Enhancers	Fetal Intestine Small	intestine
25	chr5:177888000-177888600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr5:177888000-177888600	Enhancers	Lung	lung
27	chr5:177888000-177888600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr5:177888000-177888800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr5:177888000-177888800	Enhancers	Brain Inferior Temporal Lobe	brain
30	chr5:177888000-177888800	Enhancers	Brain Substantia Nigra	brain
31	chr5:177888000-177888800	Enhancers	Duodenum Mucosa	Duodenum
32	chr5:177888000-177889000	Enhancers	Brain Hippocampus Middle	brain
33	chr5:177888000-177889200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:177888000-177889200	Enhancers	Left Ventricle	heart
35	chr5:177888000-177890400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr5:177888000-177890400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:177888000-177890600	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr5:177888000-177890800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr5:177888000-177894400	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links