Variant report

Variant	rs13014016
Chromosome Location	chr2:234257454-234257455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1000141	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs1046974	0.89[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803624	0.95[ASN][1000 genomes]
rs10803625	0.82[ASN][1000 genomes]
rs11676156	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11681192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002340	0.83[ASN][1000 genomes]
rs13003198	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241873	0.82[CHB][hapmap]
rs2289477	0.81[CHB][hapmap]
rs2879924	0.95[ASN][1000 genomes]
rs2879925	0.94[ASN][1000 genomes]
rs34595600	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34891595	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35480652	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828305	0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs67399374	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6756706	0.83[CHB][hapmap]
rs7423426	0.95[ASN][1000 genomes]
rs880114	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs880116	0.95[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]

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	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13014016	SCARNA5	cis	parietal	SCAN
rs13014016	DGKD	cis	cerebellum	SCAN
rs13014016	DGKD	Cis_1M	lymphoblastoid	RTeQTL
rs13014016	SLC16A14	cis	cerebellum	SCAN
rs13014016	DGKD	cis	lymphoblastoid	seeQTL
rs13014016	LRRC55	trans	parietal	SCAN
rs13014016	ATG16L1	cis	cerebellum	SCAN
rs13014016	SCARNA5	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234244600-234257800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:234255000-234257800	Enhancers	Brain Cingulate Gyrus	brain
3	chr2:234255000-234260000	Enhancers	Liver	Liver
4	chr2:234255400-234257600	Enhancers	Brain Anterior Caudate	brain
5	chr2:234255600-234258600	Enhancers	Brain Substantia Nigra	brain
6	chr2:234255800-234258600	Flanking Active TSS	HepG2	liver
7	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
8	chr2:234256000-234257600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:234256000-234257800	Weak transcription	K562	blood
10	chr2:234256200-234260800	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:234256400-234260400	Enhancers	Fetal Intestine Small	intestine
12	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr2:234256600-234257800	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr2:234256600-234259800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
16	chr2:234256800-234257600	Enhancers	Brain Hippocampus Middle	brain
17	chr2:234256800-234257800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr2:234256800-234258000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:234256800-234258400	Enhancers	Gastric	stomach
20	chr2:234256800-234258800	Enhancers	Brain Angular Gyrus	brain
21	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:234257000-234257600	Enhancers	Hela-S3	cervix
23	chr2:234257000-234257600	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr2:234257000-234258800	Enhancers	Fetal Muscle Trunk	muscle
25	chr2:234257000-234259200	Enhancers	Fetal Muscle Leg	muscle
26	chr2:234257000-234262200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr2:234257200-234259400	Enhancers	Fetal Thymus	thymus
28	chr2:234257200-234260000	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:234257200-234260400	Enhancers	Primary hematopoietic stem cells	blood
30	chr2:234257400-234257600	Enhancers	Colonic Mucosa	Colon
31	chr2:234257400-234257600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:234257400-234257800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:234257400-234257800	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr2:234257400-234257800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr2:234257400-234258000	Enhancers	GM12878-XiMat	blood
36	chr2:234257400-234258200	Enhancers	Primary T cells fromperipheralblood	blood
37	chr2:234257400-234258400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr2:234257400-234258400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
39	chr2:234257400-234258600	Enhancers	Placenta	Placenta
40	chr2:234257400-234258600	Enhancers	Spleen	Spleen
41	chr2:234257400-234258800	Weak transcription	Small Intestine	intestine
42	chr2:234257400-234260400	Enhancers	Fetal Intestine Large	intestine

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