Variant report

Variant	rs1230158
Chromosome Location	chr4:99990186-99990187
allele	C/T
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	POLR2A	chr4:99989742-99990360	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr4:99987204-99993723	K562	blood:	n/a	n/a
3	POLR2A	chr4:99987378-99990187	HepG2	liver:	n/a	n/a
4	FOSL2	chr4:99990079-99990340	HepG2	liver:	n/a	n/a
5	POLR2A	chr4:99989655-99990614	HepG2	liver:	n/a	n/a
6	POLR2A	chr4:99989769-99990251	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:99914968..99916800-chr4:99989851..99992126,2	MCF-7	breast:
2	chr4:99849436..99851753-chr4:99986729..99991688,5	K562	blood:

Variant related genes	Relation type
ENSG00000272777	TF binding region
ENSG00000263923	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000238449	Chromatin interaction
ENSG00000164024	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1154401	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1154403	0.86[AMR][1000 genomes]
rs1230154	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230155	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230156	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1230157	1.00[ASN][1000 genomes]
rs1230164	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1230165	1.00[ASN][1000 genomes]
rs1230167	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13832	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2602856	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2851270	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2851274	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6532796	0.81[AMR][1000 genomes]
rs6831257	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs896992	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1002927	chr4:99952472-100148690	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1005446	chr4:99988287-100121669	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv537196	chr4:99988287-100121669	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1230158	ADH5	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99954000-99999200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:99956200-99995000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:99959800-100000200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:99971800-99991600	Weak transcription	Brain Anterior Caudate	brain
5	chr4:99971800-99997600	Weak transcription	Spleen	Spleen
6	chr4:99974000-99993000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr4:99976400-99992800	Weak transcription	Aorta	Aorta
8	chr4:99977200-99994400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr4:99977400-99991600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:99977400-99992800	Weak transcription	Brain Substantia Nigra	brain
11	chr4:99977400-99994800	Weak transcription	Right Atrium	heart
12	chr4:99977400-99996600	Weak transcription	Brain Angular Gyrus	brain
13	chr4:99977400-99996800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr4:99977400-99997000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:99977600-100008400	Weak transcription	Stomach Mucosa	stomach
16	chr4:99977800-100009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr4:99978000-100007800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:99979800-99992800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:99979800-99994800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:99980000-99992600	Weak transcription	Colonic Mucosa	Colon
21	chr4:99980000-99993000	Weak transcription	Ovary	ovary
22	chr4:99980000-99995000	Weak transcription	Small Intestine	intestine
23	chr4:99980000-99997000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr4:99980200-99993000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr4:99980400-99991400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr4:99981000-99992400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr4:99981200-99992400	Weak transcription	Brain Germinal Matrix	brain
28	chr4:99981200-99997000	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:99982400-99995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr4:99982400-99997000	Weak transcription	Hela-S3	cervix
31	chr4:99982400-100000400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:99982600-99991600	Weak transcription	NHLF	lung
33	chr4:99982600-99992000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:99982600-99992400	Weak transcription	NHEK	skin
35	chr4:99982600-99992600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr4:99982600-99996000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:99982800-99993000	Weak transcription	Left Ventricle	heart
38	chr4:99982800-99996000	Weak transcription	Gastric	stomach
39	chr4:99982800-100000200	Weak transcription	Psoas Muscle	Psoas
40	chr4:99983000-99991600	Weak transcription	Brain Hippocampus Middle	brain
41	chr4:99983000-100004600	Weak transcription	Pancreas	Pancrea
42	chr4:99983200-99992400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:99983200-99992800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr4:99983200-100000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:99983200-100008800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr4:99983400-99990600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr4:99983400-99991000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr4:99983400-99992800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr4:99983400-99993000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr4:99983600-99991000	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links