Variant report

Variant	rs56861678
Chromosome Location	chr14:24407654-24407655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr14:24407649-24407795	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:24404663..24407732-chr14:24421458..24424450,4	MCF-7	breast:
2	chr14:24035516..24037456-chr14:24405967..24408124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197775	TF binding region
LINC00596	TF binding region
ENSG00000213983	Chromatin interaction
ENSG00000157326	Chromatin interaction
ENSG00000215256	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10137990	0.89[ASN][1000 genomes]
rs10137992	0.89[ASN][1000 genomes]
rs10141091	0.89[ASN][1000 genomes]
rs10142568	0.89[ASN][1000 genomes]
rs10145440	0.89[ASN][1000 genomes]
rs10148822	0.89[ASN][1000 genomes]
rs10148823	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10149094	0.89[ASN][1000 genomes]
rs10150939	0.89[ASN][1000 genomes]
rs10151793	0.89[ASN][1000 genomes]
rs11158470	0.89[ASN][1000 genomes]
rs11847840	0.89[ASN][1000 genomes]
rs11852080	0.89[ASN][1000 genomes]
rs11852089	0.89[ASN][1000 genomes]
rs12147221	0.89[ASN][1000 genomes]
rs17099424	0.89[ASN][1000 genomes]
rs17099455	0.89[ASN][1000 genomes]
rs1885809	0.89[ASN][1000 genomes]
rs1885810	0.89[ASN][1000 genomes]
rs1951736	0.89[ASN][1000 genomes]
rs1951737	0.81[AMR][1000 genomes]
rs1957678	0.89[ASN][1000 genomes]
rs2273944	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28670278	0.89[ASN][1000 genomes]
rs28693392	0.89[ASN][1000 genomes]
rs28828113	0.89[ASN][1000 genomes]
rs28836502	0.89[ASN][1000 genomes]
rs28856896	0.89[ASN][1000 genomes]
rs28881586	0.89[ASN][1000 genomes]
rs2984817	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35687405	0.89[ASN][1000 genomes]
rs4457918	0.89[ASN][1000 genomes]
rs55897938	0.89[ASN][1000 genomes]
rs57461315	0.89[ASN][1000 genomes]
rs57901513	0.89[ASN][1000 genomes]
rs57978986	0.89[ASN][1000 genomes]
rs58329055	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58786866	0.89[ASN][1000 genomes]
rs58909995	0.89[ASN][1000 genomes]
rs58920623	0.89[ASN][1000 genomes]
rs58941536	0.89[ASN][1000 genomes]
rs59434518	0.89[ASN][1000 genomes]
rs59484581	0.89[ASN][1000 genomes]
rs60177702	0.89[ASN][1000 genomes]
rs60887662	0.89[ASN][1000 genomes]
rs60901156	0.89[ASN][1000 genomes]
rs60939040	0.89[ASN][1000 genomes]
rs61368402	0.89[ASN][1000 genomes]
rs6573469	0.89[ASN][1000 genomes]
rs6573470	0.89[ASN][1000 genomes]
rs6573471	0.89[ASN][1000 genomes]
rs6573472	0.89[ASN][1000 genomes]
rs6573473	0.89[ASN][1000 genomes]
rs6573474	0.89[ASN][1000 genomes]
rs6573484	0.89[ASN][1000 genomes]
rs6573485	0.89[ASN][1000 genomes]
rs6573486	0.89[ASN][1000 genomes]
rs6573487	0.81[AMR][1000 genomes]
rs6573488	0.81[AMR][1000 genomes]
rs7140888	0.89[ASN][1000 genomes]
rs7141234	0.89[ASN][1000 genomes]
rs7141463	0.89[ASN][1000 genomes]
rs7141633	0.89[ASN][1000 genomes]
rs7141804	0.89[ASN][1000 genomes]
rs7149475	0.89[ASN][1000 genomes]
rs7152712	0.89[ASN][1000 genomes]
rs7152902	0.89[ASN][1000 genomes]
rs7153995	0.89[ASN][1000 genomes]
rs7156624	0.89[ASN][1000 genomes]
rs7158222	0.89[ASN][1000 genomes]
rs73598764	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73598777	0.89[ASN][1000 genomes]
rs73598781	0.89[ASN][1000 genomes]
rs73600715	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73600716	0.89[ASN][1000 genomes]
rs73600717	0.89[ASN][1000 genomes]
rs73600730	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs74036725	0.89[ASN][1000 genomes]
rs74036727	0.89[ASN][1000 genomes]
rs74036728	0.89[ASN][1000 genomes]
rs74036729	0.89[ASN][1000 genomes]
rs8003491	0.89[ASN][1000 genomes]
rs8003627	0.89[ASN][1000 genomes]
rs8004361	0.89[ASN][1000 genomes]
rs8004860	0.89[ASN][1000 genomes]
rs8007763	0.89[ASN][1000 genomes]
rs8009022	0.89[ASN][1000 genomes]
rs8009382	0.89[ASN][1000 genomes]
rs8009599	0.89[ASN][1000 genomes]
rs8010151	0.89[ASN][1000 genomes]
rs8011236	0.89[ASN][1000 genomes]
rs8011460	0.83[AMR][1000 genomes]
rs8022613	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9323424	0.89[ASN][1000 genomes]
rs9323425	0.89[ASN][1000 genomes]
rs9323426	0.89[ASN][1000 genomes]
rs9323428	0.89[ASN][1000 genomes]
rs9671445	0.89[ASN][1000 genomes]
rs9671467	0.89[ASN][1000 genomes]
rs9671588	0.89[ASN][1000 genomes]
rs9671870	0.89[ASN][1000 genomes]
rs9671883	0.89[ASN][1000 genomes]
rs9805875	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9805882	0.89[ASN][1000 genomes]
rs9805889	0.89[ASN][1000 genomes]
rs9805913	0.89[ASN][1000 genomes]
rs9806029	0.89[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	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
2	nsv1217	chr14:24400565-24512689	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv89	chr14:24405198-24475213	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1049316	chr14:24405420-24583724	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
5	nsv541999	chr14:24405420-24583724	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
6	esv3384545	chr14:24407544-24408123	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs56861678	DHRS4	cis	Heart Left Ventricle	GTEx
rs56861678	DHRS4	cis	Muscle Skeletal	GTEx
rs56861678	DHRS4L2	cis	Esophagus Muscularis	GTEx
rs56861678	DHRS4	cis	Adipose Subcutaneous	GTEx
rs56861678	DHRS4L2	cis	Thyroid	GTEx
rs56861678	DHRS4	cis	Thyroid	GTEx
rs56861678	DHRS4	cis	Nerve Tibial	GTEx
rs56861678	DHRS4L2	cis	Artery Tibial	GTEx
rs56861678	DHRS4L2	cis	Muscle Skeletal	GTEx
rs56861678	DHRS4	cis	Artery Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24399200-24408800	Weak transcription	Lung	lung
2	chr14:24399400-24408200	Weak transcription	Left Ventricle	heart
3	chr14:24399400-24410000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr14:24399400-24411000	Weak transcription	Brain Anterior Caudate	brain
5	chr14:24399600-24409000	Weak transcription	Brain Hippocampus Middle	brain
6	chr14:24399600-24409200	Weak transcription	Brain Germinal Matrix	brain
7	chr14:24400000-24408400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:24400000-24420000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr14:24400400-24411800	Weak transcription	HMEC	breast
10	chr14:24400600-24408600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:24400600-24408800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr14:24400600-24409600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr14:24400600-24421000	Weak transcription	Colon Smooth Muscle	Colon
14	chr14:24400800-24408600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr14:24400800-24409000	Weak transcription	Aorta	Aorta
16	chr14:24401400-24409800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr14:24401800-24409800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr14:24402200-24410000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr14:24402200-24421200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:24402400-24409800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:24403000-24408400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr14:24403000-24413200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr14:24403200-24408800	Weak transcription	Fetal Lung	lung
24	chr14:24403200-24409000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr14:24403200-24409000	Weak transcription	Fetal Stomach	stomach
26	chr14:24403200-24409200	Weak transcription	Fetal Muscle Leg	muscle
27	chr14:24403200-24409800	Weak transcription	Ovary	ovary
28	chr14:24403400-24408800	Enhancers	Liver	Liver
29	chr14:24404000-24408800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:24404800-24409400	Enhancers	HepG2	liver
31	chr14:24405000-24409200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr14:24405200-24407800	Enhancers	K562	blood
33	chr14:24405200-24411800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr14:24405400-24409800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:24405600-24411800	Weak transcription	Esophagus	oesophagus
36	chr14:24405600-24422400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr14:24405800-24408200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr14:24405800-24410000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr14:24405800-24421400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr14:24405800-24422400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr14:24406000-24408400	Weak transcription	Adipose Nuclei	Adipose
42	chr14:24406000-24410000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:24406200-24411400	Weak transcription	Stomach Mucosa	stomach
44	chr14:24406400-24409200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr14:24406600-24408200	Weak transcription	Primary T cells from cord blood	blood
46	chr14:24406600-24413400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:24406600-24416200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr14:24406800-24414600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr14:24407000-24408800	Weak transcription	Fetal Intestine Small	intestine
50	chr14:24407000-24409800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links