Variant report

Variant	rs4274186
Chromosome Location	chr11:18418719-18418720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 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	chr11:18418587-18420029	A549	lung:	n/a	n/a
3	POLR2A	chr11:18415356-18422999	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr11:18418413-18418830	HepG2	liver:	n/a	n/a
5	JUN	chr11:18418687-18418737	K562	blood:	n/a	n/a
6	POLR2A	chr11:18415438-18420199	IMR90	lung:	n/a	n/a
7	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
8	POLR2A	chr11:18415533-18418861	HepG2	liver:	n/a	n/a
9	CHD1	chr11:18415224-18419079	IMR90	lung:	n/a	n/a
10	POLR2A	chr11:18415437-18420128	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:18415524-18420304	U87	brain:	n/a	n/a
12	POLR2A	chr11:18415312-18424472	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:18415489-18420124	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:18415555-18419223	HepG2	liver:	n/a	n/a
15	HEY1	chr11:18415392-18418833	HepG2	liver:	n/a	chr11:18416059-18416068 chr11:18416057-18416066
16	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a
17	POLR2A	chr11:18418707-18418767	HUVEC	blood vessel:	n/a	n/a
18	IRF1	chr11:18417385-18418772	K562	blood:	n/a	chr11:18417790-18417804
19	POLR2A	chr11:18415580-18422609	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18415873..18420206-chr11:18430045..18435036,6	MCF-7	breast:
2	chr11:18343053..18346262-chr11:18415665..18418898,6	MCF-7	breast:
3	chr11:18416584..18419436-chr12:7046184..7047780,2	K562	blood:
4	chr11:18340586..18347042-chr11:18413380..18419628,16	K562	blood:
5	chr11:18342491..18345045-chr11:18415566..18419495,5	MCF-7	breast:
6	chr11:18362164..18364564-chr11:18417285..18419232,2	MCF-7	breast:
7	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LDHC-2	chr11:18418366-18418945	NONHSAT018284

No data

Variant related genes	Relation type
LDHA	TF binding region
ENSG00000111676	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000256006	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000166796	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 15 )

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];0.99[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];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832929	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832933	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024636	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs11024651	0.83[CHB][hapmap]
rs1830426	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]
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];0.98[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];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881717	0.87[CHB][hapmap]
rs1969562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037868	0.83[CHB][hapmap]
rs2249631	0.97[AMR][1000 genomes];1.00[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];0.99[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];0.81[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];0.99[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];0.98[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];0.99[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]
rs4820	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5030621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.98[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];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7101840	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[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];0.98[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];1.00[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];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120485	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.99[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];0.99[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];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947664	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs4274186	COPB1	cis	cerebellum	SCAN
rs4274186	TSG101	cis	lymphoblastoid	seeQTL
rs4274186	PLEKHA7	cis	parietal	SCAN
rs4274186	LDHAL6A	cis	cerebellum	SCAN
rs4274186	LDHA	cis	lymphoblastoid	GTEx
rs4274186	LDHA	cis	cerebellum	SCAN
rs4274186	RRAS2	cis	cerebellum	SCAN
rs4274186	LDHC	cis	lymphoblastoid	seeQTL
rs4274186	LDHAL6A	cis	parietal	SCAN
rs4274186	LDHC	cis	cerebellum	SCAN
rs4274186	LDHC	cis	multi-tissue	Pritchard
rs4274186	LDHC	cis	Thyroid	GTEx
rs4274186	LDHC	cis	Artery Tibial	GTEx
rs4274186	C11orf58	cis	parietal	SCAN
rs4274186	LDHC	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18416200-18418800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr11:18416200-18419800	Transcr. at gene 5' and 3'	A549	lung
3	chr11:18416200-18419800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr11:18416800-18418800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
5	chr11:18416800-18419000	Transcr. at gene 5' and 3'	K562	blood
6	chr11:18416800-18421000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:18417400-18418800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:18418000-18418800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:18418000-18418800	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr11:18418000-18418800	Transcr. at gene 5' and 3'	HSMM	muscle
11	chr11:18418000-18418800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
12	chr11:18418000-18419200	Transcr. at gene 5' and 3'	HMEC	breast
13	chr11:18418000-18420000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:18418000-18420000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:18418000-18420200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
16	chr11:18418000-18422200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
17	chr11:18418200-18418800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr11:18418200-18418800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr11:18418200-18418800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:18418200-18419000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:18418200-18419000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:18418200-18419000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:18418200-18419000	Weak transcription	Lung	lung
24	chr11:18418200-18419000	Weak transcription	Ovary	ovary
25	chr11:18418200-18419200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr11:18418200-18419200	Weak transcription	Spleen	Spleen
27	chr11:18418200-18419600	Weak transcription	Aorta	Aorta
28	chr11:18418200-18419600	Weak transcription	Gastric	stomach
29	chr11:18418200-18419800	Genic enhancers	Sigmoid Colon	Sigmoid Colon
30	chr11:18418200-18420000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:18418200-18420600	Weak transcription	Pancreas	Pancrea
32	chr11:18418200-18425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr11:18418200-18433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:18418400-18418800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
35	chr11:18418400-18418800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
36	chr11:18418400-18418800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
37	chr11:18418400-18418800	Genic enhancers	Primary hematopoietic stem cells	blood
38	chr11:18418400-18418800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:18418400-18418800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
40	chr11:18418400-18418800	Weak transcription	Brain Cingulate Gyrus	brain
41	chr11:18418400-18419000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:18418400-18419000	Weak transcription	Brain Anterior Caudate	brain
43	chr11:18418400-18419000	Weak transcription	Colonic Mucosa	Colon
44	chr11:18418400-18419200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr11:18418400-18419200	Weak transcription	Psoas Muscle	Psoas
46	chr11:18418400-18419400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr11:18418400-18419400	Weak transcription	Brain Hippocampus Middle	brain
48	chr11:18418400-18419400	Weak transcription	Thymus	Thymus
49	chr11:18418400-18419600	Enhancers	Fetal Heart	heart
50	chr11:18418400-18419800	Genic enhancers	Primary T helper cells fromperipheralblood	blood

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