Variant report

Variant	rs1830426
Chromosome Location	chr11:18419534-18419535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:18415374-18419965	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr11:18419404-18419938	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:18418587-18420029	A549	lung:	n/a	n/a
4	HEY1	chr11:18419211-18422587	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:18415356-18422999	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr11:18419260-18422165	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr11:18419345-18419805	K562	blood:	n/a	n/a
8	POLR2A	chr11:18418927-18419830	K562	blood:	n/a	n/a
9	POLR2A	chr11:18415438-18420199	IMR90	lung:	n/a	n/a
10	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
11	POLR2A	chr11:18419212-18420062	HepG2	liver:	n/a	n/a
12	POLR2A	chr11:18419444-18419732	MCF-7	breast:	n/a	n/a
13	POLR2A	chr11:18419064-18420036	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:18419278-18420079	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:18419035-18419987	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr11:18415437-18420128	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:18419519-18419700	K562	blood:	n/a	n/a
18	POLR2A	chr11:18415524-18420304	U87	brain:	n/a	n/a
19	POLR2A	chr11:18419528-18419788	HCT-116	colon:	n/a	n/a
20	POLR2A	chr11:18415312-18424472	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:18415489-18420124	GM12878	blood:	n/a	n/a
22	POLR2A	chr11:18419492-18419983	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr11:18419514-18419594	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a
25	POLR2A	chr11:18419354-18419932	HepG2	liver:	n/a	n/a
26	POLR2A	chr11:18419297-18419912	HCT-116	colon:	n/a	n/a
27	POLR2A	chr11:18415580-18422609	U87	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18415873..18420206-chr11:18430045..18435036,6	MCF-7	breast:
2	chr11:18340586..18347042-chr11:18413380..18419628,16	K562	blood:
3	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:

No data

Variant related genes	Relation type
LDHA	TF binding region
ENSG00000166796	Chromatin interaction
ENSG00000256006	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000110768	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10741744	0.91[ASN][1000 genomes]
rs10766473	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10766475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766478	0.82[ASN][1000 genomes]
rs10832927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832929	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024636	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs11024651	0.83[CHB][hapmap]
rs1881716	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881717	0.87[CHB][hapmap]
rs1969562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037868	0.83[CHB][hapmap]
rs2249631	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403278	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2403279	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2658566	0.87[CHB][hapmap]
rs2721123	0.85[AMR][1000 genomes]
rs3758680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758681	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3758682	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3758683	0.95[JPT][hapmap]
rs3781641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809096	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3809097	0.94[ASN][1000 genomes]
rs4274186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5030621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486421	1.00[ASN][1000 genomes]
rs6486425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7101840	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7106099	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7111748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112492	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7117399	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121244	1.00[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];1.00[ASN][1000 genomes]
rs7128549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7129689	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7130990	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947664	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951953	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
6	esv1811183	chr11:18389643-18432437	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1830426	LDHAL6A	cis	parietal	SCAN
rs1830426	RRAS2	cis	cerebellum	SCAN
rs1830426	C11orf58	cis	parietal	SCAN
rs1830426	LDHC	cis	parietal	SCAN
rs1830426	COPB1	cis	cerebellum	SCAN
rs1830426	LDHAL6A	cis	cerebellum	SCAN
rs1830426	LDHC	cis	cerebellum	SCAN
rs1830426	LDHA	cis	cerebellum	SCAN
rs1830426	LDHC	cis	Artery Tibial	GTEx
rs1830426	LDHA	cis	lymphoblastoid	GTEx
rs1830426	LDHC	cis	Thyroid	GTEx
rs1830426	TSG101	cis	lymphoblastoid	seeQTL
rs1830426	LDHC	cis	lymphoblastoid	seeQTL
rs1830426	PLEKHA7	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18416200-18419800	Transcr. at gene 5' and 3'	A549	lung
2	chr11:18416200-18419800	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr11:18416800-18421000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr11:18418000-18420000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:18418000-18420000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:18418000-18420200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
7	chr11:18418000-18422200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
8	chr11:18418200-18419600	Weak transcription	Aorta	Aorta
9	chr11:18418200-18419600	Weak transcription	Gastric	stomach
10	chr11:18418200-18419800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
11	chr11:18418200-18420000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:18418200-18420600	Weak transcription	Pancreas	Pancrea
13	chr11:18418200-18425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:18418200-18433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:18418400-18419600	Enhancers	Fetal Heart	heart
16	chr11:18418400-18419800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr11:18418400-18419800	Genic enhancers	Colon Smooth Muscle	Colon
18	chr11:18418400-18420000	Transcr. at gene 5' and 3'	HepG2	liver
19	chr11:18418400-18420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:18418400-18420800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:18418400-18421000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:18418400-18421800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr11:18418400-18422200	Strong transcription	Esophagus	oesophagus
24	chr11:18418400-18430600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:18418400-18430800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:18418400-18430800	Strong transcription	Left Ventricle	heart
27	chr11:18418400-18433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr11:18418600-18419600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:18418600-18419600	Genic enhancers	NHEK	skin
30	chr11:18418600-18419800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr11:18418600-18419800	Genic enhancers	NHLF	lung
32	chr11:18418600-18420200	Strong transcription	Fetal Kidney	kidney
33	chr11:18418600-18420400	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr11:18418600-18420600	Weak transcription	Fetal Brain Male	brain
35	chr11:18418600-18420800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:18418600-18420800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr11:18418600-18421200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:18418600-18422400	Strong transcription	Primary B cells from cord blood	blood
39	chr11:18418600-18422600	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr11:18418600-18422600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr11:18418600-18427800	Strong transcription	Liver	Liver
42	chr11:18418600-18428600	Strong transcription	Fetal Intestine Large	intestine
43	chr11:18418600-18429400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:18418600-18429800	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr11:18418600-18430400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:18418600-18430400	Strong transcription	Primary B cells from peripheral blood	blood
47	chr11:18418600-18430400	Strong transcription	Placenta	Placenta
48	chr11:18418600-18430400	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr11:18418600-18430400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr11:18418600-18430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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