Variant report

Variant	rs1531335
Chromosome Location	chr4:151166237-151166238
allele	C/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:4)

rs_ID	r²[population]
rs11941843	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13125688	0.86[CHB][hapmap]
rs1993656	0.84[CEU][hapmap]
rs727426	0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026797	chr4:150246932-151217137	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1022132	chr4:151162048-151183859	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1531335	DCLK2	cis	cerebellum	SCAN
rs1531335	LRBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151138800-151169800	Weak transcription	Spleen	Spleen
2	chr4:151139600-151177400	Weak transcription	Brain Substantia Nigra	brain
3	chr4:151139600-151181000	Weak transcription	Brain Angular Gyrus	brain
4	chr4:151140000-151175000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:151142200-151172200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr4:151146200-151169200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr4:151150800-151170800	Weak transcription	Pancreas	Pancrea
8	chr4:151152400-151176400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:151156200-151173000	Weak transcription	Fetal Intestine Small	intestine
10	chr4:151156400-151169000	Weak transcription	Adipose Nuclei	Adipose
11	chr4:151156400-151169400	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:151156400-151170600	Weak transcription	Right Ventricle	heart
13	chr4:151156400-151174200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:151157000-151167800	Weak transcription	Fetal Brain Female	brain
15	chr4:151157400-151167400	Weak transcription	Fetal Brain Male	brain
16	chr4:151157600-151169400	Weak transcription	Left Ventricle	heart
17	chr4:151157600-151170800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:151158000-151181000	Weak transcription	Fetal Heart	heart
19	chr4:151158200-151167800	Weak transcription	Ovary	ovary
20	chr4:151158200-151173000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:151158800-151170200	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:151159000-151173000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:151160000-151185400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:151160400-151169000	Weak transcription	NHLF	lung
25	chr4:151161200-151173000	Weak transcription	Brain Anterior Caudate	brain
26	chr4:151161600-151170800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:151161600-151177400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:151161800-151167600	Weak transcription	Fetal Stomach	stomach
29	chr4:151162000-151167600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr4:151162200-151167400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr4:151164000-151177400	Weak transcription	Placenta	Placenta
32	chr4:151164200-151169400	Weak transcription	Aorta	Aorta
33	chr4:151164200-151169600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr4:151164600-151166400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr4:151164600-151166600	Enhancers	Fetal Kidney	kidney
36	chr4:151165200-151166600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr4:151165200-151170400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr4:151165400-151166400	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr4:151165400-151166400	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr4:151165400-151166600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:151165400-151166600	Enhancers	HSMM	muscle
42	chr4:151165400-151166600	Enhancers	NH-A	brain
43	chr4:151165400-151166600	Enhancers	Osteobl	bone
44	chr4:151165600-151166400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr4:151165600-151166400	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr4:151165600-151166400	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr4:151165600-151166400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr4:151165600-151166400	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr4:151165600-151166400	Enhancers	NHDF-Ad	bronchial
50	chr4:151165600-151166600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links