Variant report

Variant	rs17099242
Chromosome Location	chr14:24400187-24400188
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:24398247..24400471-chr14:24419661..24421717,2	MCF-7	breast:
2	chr14:24195357..24197443-chr14:24399348..24402008,2	MCF-7	breast:
3	chr14:24134707..24136516-chr14:24397576..24400257,2	MCF-7	breast:
4	chr14:24399117..24400644-chr14:24401569..24403780,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259334	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10483284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099223	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17099230	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17099424	1.00[CEU][hapmap]
rs58328116	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73598744	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73598751	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73598754	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73598755	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73598756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73598757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73598759	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8005368	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8005541	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8019962	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8020121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8020612	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17099242	DHRS4L2	cis	Nerve Tibial	GTEx
rs17099242	DHRS4-AS1	cis	Artery Tibial	GTEx
rs17099242	DHRS4-AS1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24395600-24401400	Weak transcription	Fetal Kidney	kidney
2	chr14:24397800-24400400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr14:24398400-24403000	Enhancers	Fetal Intestine Small	intestine
4	chr14:24398600-24400600	Enhancers	Duodenum Smooth Muscle	Duodenum
5	chr14:24398600-24400600	Enhancers	Ovary	ovary
6	chr14:24398600-24400800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr14:24398800-24400600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:24399000-24400400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr14:24399000-24400800	Enhancers	Stomach Smooth Muscle	stomach
10	chr14:24399000-24401800	Enhancers	Liver	Liver
11	chr14:24399200-24400600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr14:24399200-24400600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:24399200-24400800	Enhancers	Fetal Stomach	stomach
14	chr14:24399200-24401000	Enhancers	K562	blood
15	chr14:24399200-24402200	Enhancers	Rectal Smooth Muscle	rectum
16	chr14:24399200-24403000	Enhancers	Fetal Intestine Large	intestine
17	chr14:24399200-24408800	Weak transcription	Lung	lung
18	chr14:24399400-24400200	Enhancers	Duodenum Mucosa	Duodenum
19	chr14:24399400-24401400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr14:24399400-24404800	Weak transcription	Pancreas	Pancrea
21	chr14:24399400-24408200	Weak transcription	Left Ventricle	heart
22	chr14:24399400-24410000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr14:24399400-24411000	Weak transcription	Brain Anterior Caudate	brain
24	chr14:24399600-24400600	Enhancers	Adipose Nuclei	Adipose
25	chr14:24399600-24409000	Weak transcription	Brain Hippocampus Middle	brain
26	chr14:24399600-24409200	Weak transcription	Brain Germinal Matrix	brain
27	chr14:24399800-24400400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr14:24399800-24400400	Enhancers	NHDF-Ad	bronchial
29	chr14:24399800-24400600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr14:24399800-24400600	Enhancers	Osteobl	bone
31	chr14:24400000-24400400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:24400000-24400400	Enhancers	Fetal Lung	lung
33	chr14:24400000-24400400	Enhancers	HMEC	breast
34	chr14:24400000-24400600	Enhancers	Colon Smooth Muscle	Colon
35	chr14:24400000-24400800	Enhancers	Aorta	Aorta
36	chr14:24400000-24401200	Weak transcription	HepG2	liver
37	chr14:24400000-24401600	Enhancers	Stomach Mucosa	stomach
38	chr14:24400000-24408400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr14:24400000-24420000	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links