Variant report

Variant	rs613993
Chromosome Location	chr18:12028580-12028581
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	chr18:12028439-12029021	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr18:12028127-12028800	HL-60	blood:	n/a	n/a
3	POLR2A	chr18:12027940-12028956	Hela-S3	cervix:	n/a	n/a
4	USF2	chr18:12028326-12028602	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr18:12028205-12028679	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
IMPA2	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1036903	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1036904	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11876652	0.81[JPT][hapmap]
rs1250171	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1530368	0.92[ASN][1000 genomes]
rs1662607	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1662612	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs1662613	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1964436	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2006690	0.81[JPT][hapmap]
rs2075826	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs2849393	0.81[JPT][hapmap]
rs2849414	0.81[JPT][hapmap]
rs2849415	0.80[JPT][hapmap]
rs2849416	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2849418	0.81[JPT][hapmap]
rs2851900	0.80[JPT][hapmap]
rs2851901	0.80[JPT][hapmap]
rs2851915	0.85[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2851916	0.87[ASN][1000 genomes]
rs2851922	0.81[JPT][hapmap]
rs2851928	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2851930	0.85[ASN][1000 genomes]
rs4797615	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs56076781	0.88[ASN][1000 genomes]
rs583965	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs594235	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs596081	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs596142	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597072	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597094	0.87[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597147	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597965	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs597973	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs598005	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs609104	0.94[ASN][1000 genomes]
rs609588	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs627448	0.92[ASN][1000 genomes]
rs627492	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs640088	0.87[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6505710	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs655840	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs656193	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs674758	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs687869	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7236715	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs949233	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv2758470	chr18:11897023-12076102	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	esv2758713	chr18:11897023-12076102	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv909384	chr18:11907374-12101109	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv909386	chr18:11938102-12095950	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv909388	chr18:11987988-12141372	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv909389	chr18:11987988-12141625	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv909390	chr18:11987988-12155371	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv528699	chr18:11989416-12029857	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv909391	chr18:11989416-12146408	Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	nsv909392	chr18:11989416-12146698	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	nsv909393	chr18:12001258-12155371	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
14	nsv909394	chr18:12017343-12141372	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11982600-12028600	Weak transcription	Small Intestine	intestine
2	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
3	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
4	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr18:11998800-12029400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr18:11999000-12034000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr18:11999200-12035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr18:12015800-12030400	Strong transcription	Fetal Stomach	stomach
11	chr18:12016000-12032400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr18:12016000-12032400	Weak transcription	HSMM	muscle
13	chr18:12016200-12038000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr18:12016400-12030200	Weak transcription	Fetal Kidney	kidney
15	chr18:12016400-12032600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr18:12016600-12032400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:12017600-12031800	Weak transcription	Osteobl	bone
18	chr18:12017600-12038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr18:12021200-12029800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr18:12022600-12029000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr18:12023000-12033400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr18:12023200-12033600	Strong transcription	Fetal Intestine Small	intestine
23	chr18:12023400-12033000	Weak transcription	HSMMtube	muscle
24	chr18:12023600-12028600	Weak transcription	Ovary	ovary
25	chr18:12023600-12029800	Weak transcription	A549	lung
26	chr18:12023800-12031400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:12024200-12038400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr18:12025600-12030000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr18:12026400-12029000	Enhancers	HMEC	breast
30	chr18:12026400-12029200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr18:12026600-12028600	Enhancers	Esophagus	oesophagus
32	chr18:12026600-12029200	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr18:12026800-12029200	Genic enhancers	Fetal Muscle Trunk	muscle
34	chr18:12026800-12031400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr18:12027000-12029000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr18:12027000-12029000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr18:12027000-12032000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr18:12027200-12028600	Weak transcription	Colon Smooth Muscle	Colon
39	chr18:12027200-12033400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr18:12027400-12028600	Weak transcription	Right Atrium	heart
41	chr18:12027400-12029000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr18:12027400-12030400	Weak transcription	Left Ventricle	heart
43	chr18:12027400-12031200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr18:12027400-12032000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr18:12027400-12033800	Strong transcription	Hela-S3	cervix
46	chr18:12027400-12038400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr18:12027600-12029000	Enhancers	NHEK	skin
48	chr18:12027600-12029600	Weak transcription	Stomach Mucosa	stomach
49	chr18:12027800-12029000	Strong transcription	Fetal Lung	lung
50	chr18:12027800-12031200	Strong transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links