Variant report

Variant	rs3758682
Chromosome Location	chr11:18429467-18429468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:18429359-18430999	PANC-1	pancreas:	n/a	n/a
2	CEBPB	chr11:18429018-18429652	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:18429310-18430390	K562	blood:	n/a	n/a
4	BCL3	chr11:18428976-18431218	A549	lung:	n/a	n/a
5	MYBL2	chr11:18428852-18430850	HepG2	liver:	n/a	n/a
6	MBD4	chr11:18429312-18430964	HepG2	liver:	n/a	n/a
7	POLR2A	chr11:18428179-18429478	GM12878	blood:	n/a	n/a
8	CEBPB	chr11:18429060-18429676	A549	lung:	n/a	n/a
9	POLR2A	chr11:18426330-18430949	HepG2	liver:	n/a	n/a
10	POLR2A	chr11:18428646-18430926	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:18428761-18430848	HepG2	liver:	n/a	n/a
12	ARID3A	chr11:18429056-18429644	HepG2	liver:	n/a	n/a
13	POLR2A	chr11:18428875-18431440	A549	lung:	n/a	n/a
14	HEY1	chr11:18428579-18430903	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:18428498-18431298	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr11:18428955-18430921	K562	blood:	n/a	n/a
17	POLR2A	chr11:18429311-18430957	HL-60	blood:	n/a	n/a
18	CEBPB	chr11:18429308-18429653	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
20	MBD4	chr11:18428935-18430840	HepG2	liver:	n/a	n/a
21	POLR2A	chr11:18426347-18431429	PFSK-1	brain:	n/a	n/a
22	CEBPB	chr11:18429349-18429650	K562	blood:	n/a	n/a
23	POLR2A	chr11:18428177-18432634	U87	brain:	n/a	n/a
24	STAT3	chr11:18429101-18429524	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr11:18428618-18431000	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr11:18429465-18430759	K562	blood:	n/a	n/a
27	FOSL2	chr11:18428926-18429490	A549	lung:	n/a	chr11:18429197-18429208
28	PML	chr11:18429342-18430622	K562	blood:	n/a	n/a
29	POLR2A	chr11:18428440-18431439	GM12891	blood:	n/a	n/a
30	CEBPB	chr11:18429392-18429612	IMR90	lung:	n/a	n/a
31	POLR2A	chr11:18428593-18431268	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr11:18429022-18430855	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr11:18428589-18431070	K562	blood:	n/a	n/a
34	POLR2A	chr11:18426688-18431044	HepG2	liver:	n/a	n/a
35	POLR2A	chr11:18428444-18431399	K562	blood:	n/a	n/a
36	POLR2A	chr11:18428323-18432585	GM12878	blood:	n/a	n/a
37	FOS	chr11:18429025-18429616	MCF10A-Er-Src	breast:	n/a	n/a
38	FOSL2	chr11:18428957-18429498	HepG2	liver:	n/a	chr11:18429197-18429208
39	TEAD4	chr11:18429361-18429880	K562	blood:	n/a	n/a
40	POLR2A	chr11:18429466-18431465	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr11:18428613-18431437	HepG2	liver:	n/a	n/a
42	POLR2A	chr11:18429347-18430961	HCT-116	colon:	n/a	n/a
43	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a
44	POLR2A	chr11:18429435-18430866	K562	blood:	n/a	n/a
45	POLR2A	chr11:18429384-18431438	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr11:18428219-18430758	K562	blood:	n/a	n/a
47	POLR2A	chr11:18428609-18431544	SK-N-SH	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18398568..18400836-chr11:18427462..18430326,2	MCF-7	breast:
2	chr11:18406695..18409198-chr11:18428247..18430111,2	K562	blood:
3	chr11:18415543..18417980-chr11:18429058..18431461,3	K562	blood:
4	chr11:18428578..18433796-chr11:18433952..18441799,12	K562	blood:
5	chr11:18415665..18418550-chr11:18429109..18431220,2	MCF-7	breast:
6	chr11:18429091..18432597-chr11:18437736..18442022,5	K562	blood:
7	chr11:18419996..18422097-chr11:18428785..18430371,2	K562	blood:
8	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:
9	chr11:18429142..18431296-chr11:18432609..18435165,2	K562	blood:
10	chr11:18423297..18429050-chr11:18429237..18433863,11	K562	blood:

No data

Variant related genes	Relation type
LDHC	TF binding region
ENSG00000134333	Chromatin interaction
ENSG00000256006	Chromatin interaction
ENSG00000166796	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10741744	0.88[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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10766478	0.83[ASN][1000 genomes]
rs10832927	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832929	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832931	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832932	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832933	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024636	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs11024651	0.83[CHB][hapmap]
rs1830426	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]
rs1881716	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];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1881717	0.87[CHB][hapmap]
rs1969562	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969563	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037868	0.83[CHB][hapmap]
rs2249631	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.97[ASN][1000 genomes]
rs2658566	0.87[CHB][hapmap]
rs2721123	0.87[AMR][1000 genomes]
rs3758680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758681	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3758683	0.95[JPT][hapmap]
rs3781641	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];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3809096	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs3809097	0.96[ASN][1000 genomes]
rs4274186	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]
rs4820	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5030621	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486421	0.97[ASN][1000 genomes]
rs6486425	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];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7101840	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7106099	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7112492	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7117399	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120485	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7121244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs7128549	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7129689	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7130990	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947664	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7951953	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv982991	chr11:18424852-18431306	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs3758682	LDHAL6A	cis	cerebellum	SCAN
rs3758682	LDHC	cis	parietal	SCAN
rs3758682	LDHC	cis	cerebellum	SCAN
rs3758682	LDHA	cis	cerebellum	SCAN
rs3758682	C11orf58	cis	parietal	SCAN
rs3758682	TSG101	cis	lymphoblastoid	seeQTL
rs3758682	LDHC	cis	Thyroid	GTEx
rs3758682	LDHA	cis	lymphoblastoid	GTEx
rs3758682	COPB1	cis	cerebellum	SCAN
rs3758682	LDHC	cis	Artery Tibial	GTEx
rs3758682	PLEKHA7	cis	parietal	SCAN
rs3758682	LDHC	cis	lymphoblastoid	seeQTL
rs3758682	LDHAL6A	cis	parietal	SCAN
rs3758682	LDHC	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18418200-18433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18418400-18430600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr11:18418400-18430800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr11:18418400-18430800	Strong transcription	Left Ventricle	heart
5	chr11:18418400-18433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:18418600-18429800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr11:18418600-18430400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:18418600-18430400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr11:18418600-18430400	Strong transcription	Placenta	Placenta
10	chr11:18418600-18430400	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr11:18418600-18430400	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:18418600-18430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:18418600-18430600	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr11:18418600-18430600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr11:18418600-18430800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr11:18418600-18430800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr11:18418600-18430800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr11:18418600-18430800	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr11:18418600-18430800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:18418600-18430800	Strong transcription	Fetal Muscle Leg	muscle
21	chr11:18418600-18430800	Strong transcription	Fetal Stomach	stomach
22	chr11:18418600-18430800	Strong transcription	Fetal Thymus	thymus
23	chr11:18418600-18430800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr11:18418600-18430800	Strong transcription	Right Ventricle	heart
25	chr11:18418800-18430400	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:18418800-18430600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:18418800-18430600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr11:18418800-18430600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:18418800-18430600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr11:18418800-18430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:18418800-18430800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr11:18418800-18430800	Strong transcription	Adipose Nuclei	Adipose
33	chr11:18418800-18430800	Strong transcription	Osteobl	bone
34	chr11:18418800-18431000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:18419000-18430000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:18419000-18430400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:18419000-18430600	Strong transcription	Duodenum Mucosa	Duodenum
38	chr11:18419000-18430800	Strong transcription	Brain Anterior Caudate	brain
39	chr11:18419000-18430800	Strong transcription	Fetal Intestine Small	intestine
40	chr11:18419000-18431400	Strong transcription	HSMM	muscle
41	chr11:18419200-18430400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:18419200-18430400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:18419200-18430400	Strong transcription	Rectal Smooth Muscle	rectum
44	chr11:18419200-18430600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr11:18419200-18430600	Strong transcription	Spleen	Spleen
46	chr11:18419400-18430200	Strong transcription	HUVEC	blood vessel
47	chr11:18419400-18430400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:18419600-18430800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:18419800-18430200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:18419800-18430200	Strong transcription	Muscle Satellite Cultured Cells	--

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