Variant report

Variant	rs62347029
Chromosome Location	chr4:151288860-151288861
allele	A/T
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:2)

rs_ID	r²[population]
rs2290846	0.83[AMR][1000 genomes]
rs56374126	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932022	chr4:150831733-151419552	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1032689	chr4:150971003-151316856	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv537300	chr4:150971003-151316856	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv880259	chr4:151210761-151367745	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv880260	chr4:151214038-151331191	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv830112	chr4:151243801-151431771	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62347029	DCLK2	cis	Whole Blood	GTEx
rs62347029	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151243000-151312000	Weak transcription	Primary B cells from cord blood	blood
2	chr4:151244200-151300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:151262400-151311200	Weak transcription	Primary T cells from cord blood	blood
4	chr4:151268800-151293800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:151269800-151300600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:151272000-151293800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:151272000-151298600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:151272000-151371400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr4:151272400-151294000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:151279200-151298000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr4:151280600-151289200	Weak transcription	Fetal Lung	lung
12	chr4:151285600-151297600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:151286200-151290600	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:151286600-151355600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr4:151287400-151289000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:151287400-151290200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:151287800-151289200	Weak transcription	K562	blood
18	chr4:151288000-151289400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:151288000-151289800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:151288200-151289200	Weak transcription	Fetal Heart	heart
21	chr4:151288200-151289400	Enhancers	Fetal Stomach	stomach
22	chr4:151288200-151290400	Weak transcription	Ovary	ovary
23	chr4:151288400-151289000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr4:151288400-151290600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr4:151288600-151289000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
26	chr4:151288600-151289000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
27	chr4:151288600-151289200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr4:151288600-151289200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
29	chr4:151288600-151289800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr4:151288600-151291200	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr4:151288800-151289000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
32	chr4:151288800-151289000	Active TSS	Colon Smooth Muscle	Colon
33	chr4:151288800-151289000	Enhancers	Fetal Kidney	kidney
34	chr4:151288800-151289600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
35	chr4:151288800-151289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:151288800-151289800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:151288800-151289800	Weak transcription	Stomach Smooth Muscle	stomach

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