Variant report

Variant	rs7130990
Chromosome Location	chr11:18420254-18420255
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	chr11:18419958-18420274	A549	lung:	n/a	n/a
2	POLR2A	chr11:18420163-18420299	A549	lung:	n/a	n/a
3	HEY1	chr11:18419211-18422587	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:18415356-18422999	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr11:18419260-18422165	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
7	POLR2A	chr11:18419895-18420908	K562	blood:	n/a	n/a
8	POLR2A	chr11:18415524-18420304	U87	brain:	n/a	n/a
9	POLR2A	chr11:18415312-18424472	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:18420249-18422882	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a
12	PAX5	chr11:18419928-18420263	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:18420122-18420317	HepG2	liver:	n/a	n/a
14	POLR2A	chr11:18415580-18422609	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:

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

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10741744	0.91[ASN][1000 genomes]
rs10766475	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766478	0.82[ASN][1000 genomes]
rs10832927	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832929	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832931	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832932	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832933	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1830426	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881716	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969562	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969563	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249631	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403279	1.00[ASN][1000 genomes]
rs2721123	0.83[AMR][1000 genomes]
rs3758680	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758682	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781641	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809096	0.90[ASN][1000 genomes]
rs3809097	0.94[ASN][1000 genomes]
rs4274186	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5030621	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486421	1.00[ASN][1000 genomes]
rs6486425	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7101840	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7106099	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7111748	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112492	0.96[ASN][1000 genomes]
rs7117399	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120485	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121244	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128549	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947664	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7130990	LDHC	cis	Thyroid	GTEx
rs7130990	LDHC	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18416800-18421000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr11:18418000-18422200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
3	chr11:18418200-18420600	Weak transcription	Pancreas	Pancrea
4	chr11:18418200-18425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:18418200-18433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr11:18418400-18420400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr11:18418400-18420800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:18418400-18421000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr11:18418400-18421800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:18418400-18422200	Strong transcription	Esophagus	oesophagus
11	chr11:18418400-18430600	Strong transcription	Fetal Muscle Trunk	muscle
12	chr11:18418400-18430800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:18418400-18430800	Strong transcription	Left Ventricle	heart
14	chr11:18418400-18433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr11:18418600-18420400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr11:18418600-18420600	Weak transcription	Fetal Brain Male	brain
17	chr11:18418600-18420800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:18418600-18420800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
19	chr11:18418600-18421200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr11:18418600-18422400	Strong transcription	Primary B cells from cord blood	blood
21	chr11:18418600-18422600	Strong transcription	Brain Inferior Temporal Lobe	brain
22	chr11:18418600-18422600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr11:18418600-18427800	Strong transcription	Liver	Liver
24	chr11:18418600-18428600	Strong transcription	Fetal Intestine Large	intestine
25	chr11:18418600-18429400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:18418600-18429800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr11:18418600-18430400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr11:18418600-18430400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr11:18418600-18430400	Strong transcription	Placenta	Placenta
30	chr11:18418600-18430400	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr11:18418600-18430400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:18418600-18430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:18418600-18430600	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr11:18418600-18430600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr11:18418600-18430800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr11:18418600-18430800	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr11:18418600-18430800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:18418600-18430800	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:18418600-18430800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:18418600-18430800	Strong transcription	Fetal Muscle Leg	muscle
41	chr11:18418600-18430800	Strong transcription	Fetal Stomach	stomach
42	chr11:18418600-18430800	Strong transcription	Fetal Thymus	thymus
43	chr11:18418600-18430800	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr11:18418600-18430800	Strong transcription	Right Ventricle	heart
45	chr11:18418800-18420600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
46	chr11:18418800-18422000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr11:18418800-18422600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:18418800-18422600	Strong transcription	Brain Cingulate Gyrus	brain
49	chr11:18418800-18422800	Strong transcription	NH-A	brain
50	chr11:18418800-18427400	Strong transcription	Primary hematopoietic stem cells	blood

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