Variant report

Variant	rs609588
Chromosome Location	chr18:12034196-12034197
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	chr18:12034185-12034272	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12028430..12032053-chr18:12032793..12035686,4	K562	blood:
2	chr18:12028306..12030912-chr18:12032872..12035314,2	K562	blood:

Variant related genes	Relation type
ENSG00000267480	TF binding region
ENSG00000141401	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1036903	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1036904	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11876652	0.80[JPT][hapmap]
rs1250171	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1530368	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1662607	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662613	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1964436	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2006690	0.80[JPT][hapmap]
rs2075826	0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2849393	0.80[JPT][hapmap]
rs2849414	0.80[JPT][hapmap]
rs2849416	0.85[JPT][hapmap]
rs2849418	0.80[JPT][hapmap]
rs2851915	0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2851916	0.91[ASN][1000 genomes]
rs2851922	0.80[JPT][hapmap];1.00[YRI][hapmap]
rs2851928	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851930	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797615	0.85[JPT][hapmap]
rs56076781	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs583965	0.81[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs594235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596142	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597072	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597094	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597147	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597965	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597973	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609104	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613993	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs627448	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627492	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs640088	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505710	0.85[JPT][hapmap]
rs655840	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs656193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs674758	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs687869	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231547	0.82[YRI][hapmap]
rs7236715	0.85[JPT][hapmap]
rs949233	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
11	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
12	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
13	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:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11996600-12035000	Weak transcription	Primary T cells from cord blood	blood
2	chr18:11996800-12034400	Weak transcription	Primary B cells from cord blood	blood
3	chr18:11997000-12034400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr18:11999200-12035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr18:12016200-12038000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr18:12017600-12038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:12024200-12038400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr18:12027400-12038400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:12028000-12034400	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr18:12028200-12035200	Strong transcription	Liver	Liver
12	chr18:12028800-12034200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr18:12028800-12038200	Weak transcription	Psoas Muscle	Psoas
14	chr18:12028800-12038400	Weak transcription	Right Atrium	heart
15	chr18:12029000-12034600	Strong transcription	Pancreas	Pancrea
16	chr18:12029000-12036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr18:12029000-12037400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr18:12029000-12038000	Weak transcription	HMEC	breast
19	chr18:12029000-12038200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr18:12029800-12034600	Strong transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:12030200-12035000	Weak transcription	Thymus	Thymus
22	chr18:12030200-12038200	Weak transcription	Ovary	ovary
23	chr18:12030600-12038000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr18:12030600-12038400	Weak transcription	Lung	lung
25	chr18:12030800-12038000	Weak transcription	A549	lung
26	chr18:12031000-12035200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr18:12031200-12035600	Weak transcription	HepG2	liver
28	chr18:12031200-12038000	Weak transcription	Colonic Mucosa	Colon
29	chr18:12031200-12038200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr18:12031400-12035000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr18:12031400-12038000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr18:12031400-12038000	Weak transcription	Fetal Intestine Large	intestine
33	chr18:12031400-12038200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr18:12031400-12038200	Weak transcription	Stomach Mucosa	stomach
35	chr18:12031400-12038200	Weak transcription	Spleen	Spleen
36	chr18:12031400-12038800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr18:12031800-12038400	Weak transcription	Aorta	Aorta
38	chr18:12032000-12035200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr18:12032000-12037800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr18:12032000-12038200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr18:12032200-12036400	Weak transcription	NHEK	skin
42	chr18:12032200-12038200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr18:12032400-12036400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr18:12032400-12038000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr18:12032400-12038400	Weak transcription	Fetal Lung	lung
46	chr18:12032600-12038000	Weak transcription	Colon Smooth Muscle	Colon
47	chr18:12032600-12038400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:12033000-12034200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr18:12033000-12034800	Strong transcription	Right Ventricle	heart
50	chr18:12033000-12035600	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links