Variant report

Variant	rs17324501
Chromosome Location	chr2:30979720-30979721
allele	C/T
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	chr2:30974357..30976391-chr2:30976860..30980887,3	K562	blood:
2	chr2:30971328..30973922-chr2:30977969..30979743,3	MCF-7	breast:
3	chr2:30974420..30976391-chr2:30977915..30980887,2	K562	blood:
4	chr2:30977562..30982184-chr2:31026694..31034377,7	MCF-7	breast:
5	chr2:30967775..30969478-chr2:30977702..30980114,2	MCF-7	breast:
6	chr2:30977154..30980117-chr2:31067172..31070017,2	MCF-7	breast:
7	chr2:30978342..30980549-chr2:31003793..31005445,2	MCF-7	breast:
8	chr2:30978882..30982474-chr2:30994656..30997998,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162949	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11127287	0.81[EUR][1000 genomes]
rs11674967	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245770	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv873770	chr2:30952987-30984850	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv520269	chr2:30958137-30988375	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv456019	chr2:30968228-30984850	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
5	nsv581267	chr2:30968228-30984850	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17324501	PREB	cis	parietal	SCAN
rs17324501	CLIP4	cis	parietal	SCAN
rs17324501	DPY30	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30960400-30980000	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:30965800-30999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:30968200-30985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:30971000-30984800	Weak transcription	Stomach Mucosa	stomach
5	chr2:30978000-30980800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:30978200-30980000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:30978200-30980200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:30978400-30980800	Enhancers	Pancreas	Pancrea
9	chr2:30978400-30981200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:30978600-30979800	Enhancers	NHEK	skin
11	chr2:30978600-30984600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr2:30978800-30979800	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:30978800-30979800	Enhancers	Small Intestine	intestine
14	chr2:30978800-30980200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:30978800-30980200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr2:30978800-30980600	Enhancers	Fetal Muscle Leg	muscle
17	chr2:30978800-30980600	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr2:30979000-30979800	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr2:30979000-30979800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:30979000-30980000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:30979000-30980400	Weak transcription	Spleen	Spleen
22	chr2:30979000-30980600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr2:30979200-30980000	Genic enhancers	Gastric	stomach
24	chr2:30979200-30980400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:30979200-30981600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:30979600-30980600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr2:30979600-30980600	Weak transcription	NHDF-Ad	bronchial
28	chr2:30979600-30981400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr2:30979600-30985000	Weak transcription	Fetal Intestine Small	intestine
30	chr2:30979600-30985400	Weak transcription	Duodenum Mucosa	Duodenum

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