Variant report

Variant	rs596081
Chromosome Location	chr18:12033444-12033445
allele	G/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	chr18:12033332-12033837	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr18:12033285-12033637	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr18:12032933-12033466	Hela-S3	cervix:	n/a	n/a
4	MAFK	chr18:12033048-12033460	IMR90	lung:	n/a	chr18:12033287-12033296
5	JUND	chr18:12033096-12033504	Hela-S3	cervix:	n/a	chr18:12033284-12033296 chr18:12033286-12033295 chr18:12033284-12033295 chr18:12033285-12033295 chr18:12033286-12033294 chr18:12033287-12033294

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: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1036903	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1036904	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11876652	0.85[JPT][hapmap]
rs1250171	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1530368	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1662607	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1662612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1662613	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1964436	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2006690	0.85[JPT][hapmap]
rs2075826	0.94[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2849393	0.85[JPT][hapmap]
rs2849414	0.85[JPT][hapmap]
rs2849415	0.85[JPT][hapmap]
rs2849416	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2849418	0.85[JPT][hapmap]
rs2849420	0.83[JPT][hapmap]
rs2851900	0.85[JPT][hapmap]
rs2851901	0.85[JPT][hapmap]
rs2851915	0.85[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2851916	0.90[ASN][1000 genomes]
rs2851922	0.85[JPT][hapmap]
rs2851928	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851930	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4797615	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs56076781	0.91[ASN][1000 genomes]
rs583965	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs594235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs596142	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597072	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597094	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597147	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597965	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs597973	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs598005	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609104	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs609588	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]
rs613993	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]
rs627448	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs627492	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs640088	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505710	0.88[CHD][hapmap];0.85[JPT][hapmap]
rs655840	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs656193	0.86[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs674758	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs687869	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7231547	0.85[YRI][hapmap]
rs7236715	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs949233	0.85[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs596081	CLC	trans	parietal	SCAN

Chromatin state (count:94 , 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	chr18:11998400-12034000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr18:11999000-12034000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr18:11999000-12035400	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr18:11999200-12035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr18:12016200-12038000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr18:12017600-12038400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr18:12023200-12033600	Strong transcription	Fetal Intestine Small	intestine
11	chr18:12024200-12038400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr18:12027400-12033800	Strong transcription	Hela-S3	cervix
13	chr18:12027400-12038400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr18:12028000-12034400	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr18:12028200-12035200	Strong transcription	Liver	Liver
16	chr18:12028800-12034000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr18:12028800-12034200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr18:12028800-12038200	Weak transcription	Psoas Muscle	Psoas
19	chr18:12028800-12038400	Weak transcription	Right Atrium	heart
20	chr18:12029000-12034600	Strong transcription	Pancreas	Pancrea
21	chr18:12029000-12036000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr18:12029000-12037400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr18:12029000-12038000	Weak transcription	HMEC	breast
24	chr18:12029000-12038200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr18:12029800-12034600	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr18:12030200-12035000	Weak transcription	Thymus	Thymus
27	chr18:12030200-12038200	Weak transcription	Ovary	ovary
28	chr18:12030400-12034000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr18:12030600-12038000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr18:12030600-12038400	Weak transcription	Lung	lung
31	chr18:12030800-12038000	Weak transcription	A549	lung
32	chr18:12031000-12035200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:12031200-12034000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr18:12031200-12035600	Weak transcription	HepG2	liver
35	chr18:12031200-12038000	Weak transcription	Colonic Mucosa	Colon
36	chr18:12031200-12038200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr18:12031400-12033800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr18:12031400-12034000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr18:12031400-12035000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr18:12031400-12038000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:12031400-12038000	Weak transcription	Fetal Intestine Large	intestine
42	chr18:12031400-12038200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr18:12031400-12038200	Weak transcription	Stomach Mucosa	stomach
44	chr18:12031400-12038200	Weak transcription	Spleen	Spleen
45	chr18:12031400-12038800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr18:12031800-12034000	Strong transcription	Fetal Muscle Leg	muscle
47	chr18:12031800-12034000	Enhancers	NHDF-Ad	bronchial
48	chr18:12031800-12034000	Enhancers	Osteobl	bone
49	chr18:12031800-12038400	Weak transcription	Aorta	Aorta
50	chr18:12032000-12033600	Weak transcription	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links