Variant report

Variant	rs56090313
Chromosome Location	chr18:44679836-44679837
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	POLR2A	chr18:44679294-44680088	K562	blood:	n/a	n/a
2	POLR2A	chr18:44679825-44680104	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr18:44678500-44681193	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
HDHD2	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11872350	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11872528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11873174	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11874348	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875258	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11876118	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876495	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11877963	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878050	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55704228	1.00[AFR][1000 genomes]
rs55717985	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55823165	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55890037	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56055727	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs66875245	1.00[ASN][1000 genomes]
rs67918319	1.00[ASN][1000 genomes]
rs72903209	0.81[EUR][1000 genomes]
rs72903212	0.80[AMR][1000 genomes]
rs72903231	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72903232	0.81[EUR][1000 genomes]
rs72903252	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72903283	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72903284	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72903301	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905404	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905405	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905406	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905408	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905410	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905422	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905430	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72905433	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905469	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905471	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905478	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905489	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905490	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72905500	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907205	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907208	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907211	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907215	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907257	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907259	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907266	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72907274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909234	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909287	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72909295	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911209	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72919256	0.80[AMR][1000 genomes]
rs72921363	0.81[EUR][1000 genomes]
rs72921366	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44677600-44680200	Weak transcription	Fetal Intestine Large	intestine
2	chr18:44677600-44685400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:44677600-44700200	Weak transcription	Aorta	Aorta
4	chr18:44677800-44680000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr18:44677800-44680000	Weak transcription	Placenta	Placenta
6	chr18:44677800-44680200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr18:44677800-44680200	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr18:44677800-44680400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr18:44677800-44680400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr18:44677800-44680400	Weak transcription	Fetal Thymus	thymus
11	chr18:44677800-44680400	Weak transcription	Ovary	ovary
12	chr18:44677800-44680400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr18:44677800-44680400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr18:44677800-44680600	Weak transcription	HMEC	breast
15	chr18:44677800-44680800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr18:44677800-44681000	Weak transcription	Brain Germinal Matrix	brain
17	chr18:44677800-44682800	Weak transcription	Colonic Mucosa	Colon
18	chr18:44677800-44684800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr18:44677800-44685600	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr18:44677800-44686400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr18:44677800-44686600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr18:44677800-44686600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr18:44677800-44689800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr18:44677800-44693400	Weak transcription	Gastric	stomach
25	chr18:44677800-44698200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr18:44677800-44699000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr18:44677800-44700400	Weak transcription	Spleen	Spleen
28	chr18:44677800-44701000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:44677800-44701000	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr18:44677800-44701000	Weak transcription	A549	lung
31	chr18:44677800-44701800	Weak transcription	Esophagus	oesophagus
32	chr18:44678000-44680000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr18:44678000-44680000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr18:44678000-44680000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr18:44678000-44680200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr18:44678000-44680200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr18:44678000-44680200	Weak transcription	Fetal Kidney	kidney
38	chr18:44678000-44680200	Weak transcription	Osteobl	bone
39	chr18:44678000-44680400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr18:44678000-44680400	Weak transcription	Primary B cells from cord blood	blood
41	chr18:44678000-44680400	Weak transcription	Brain Anterior Caudate	brain
42	chr18:44678000-44680400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr18:44678000-44680600	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr18:44678000-44681600	Weak transcription	Brain Hippocampus Middle	brain
45	chr18:44678000-44682200	Weak transcription	Fetal Brain Female	brain
46	chr18:44678000-44682800	Weak transcription	Brain Substantia Nigra	brain
47	chr18:44678000-44683400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr18:44678000-44684400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr18:44678000-44687000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr18:44678000-44689200	Weak transcription	GM12878-XiMat	blood

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