Variant report

Variant	rs642624
Chromosome Location	chr5:177969010-177969011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs472238	0.81[CHB][hapmap]
rs504596	0.90[JPT][hapmap]
rs564195	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	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
5	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
6	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
7	nsv883215	chr5:177961860-177980792	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs642624	SQSTM1	cis	parietal	SCAN
rs642624	NSD1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177954600-177973800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:177960400-177969400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:177963000-177971200	Weak transcription	Right Atrium	heart
4	chr5:177965200-177969400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr5:177965200-177971600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:177965600-177969400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr5:177965800-177972400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr5:177966000-177969400	Weak transcription	Fetal Lung	lung
9	chr5:177967200-177969400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr5:177968000-177970600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:177968400-177970800	Enhancers	Fetal Stomach	stomach
12	chr5:177968600-177969800	Enhancers	Fetal Heart	heart
13	chr5:177968600-177979400	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr5:177968800-177969200	Enhancers	Left Ventricle	heart
15	chr5:177968800-177969200	Enhancers	Right Ventricle	heart
16	chr5:177968800-177970200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:177968800-177970200	Enhancers	Stomach Smooth Muscle	stomach
18	chr5:177968800-177970600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr5:177968800-177971200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr5:177968800-177974600	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links