Variant report

Variant	rs3809097
Chromosome Location	chr11:18433780-18433781
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:122)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr11:18433633-18434011	A549	lung:	n/a	n/a
2	E2F6	chr11:18433654-18434108	A549	lung:	n/a	chr11:18433801-18433810
3	MAX	chr11:18433686-18434039	HUVEC	blood vessel:	n/a	n/a
4	E2F6	chr11:18433520-18434234	A549	lung:	n/a	chr11:18433801-18433810
5	CTCF	chr11:18433680-18433830	HCPEpiC	choroid plexus:	n/a	chr11:18433802-18433815
6	MAX	chr11:18433633-18434174	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr11:18433591-18434097	GM15510	blood:	n/a	n/a
8	MAX	chr11:18433662-18434085	SK-N-SH	brain:	n/a	n/a
9	JUND	chr11:18433752-18433899	H1-hESC	embryonic stem cell:	n/a	n/a
10	USF2	chr11:18433733-18433935	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr11:18433707-18434096	H1-hESC	embryonic stem cell:	n/a	n/a
12	MAX	chr11:18433556-18434172	A549	lung:	n/a	n/a
13	POLR2A	chr11:18433682-18433991	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr11:18433586-18434098	GM18951	blood:	n/a	n/a
15	MAX	chr11:18433617-18434188	SK-N-SH	brain:	n/a	n/a
16	CREB1	chr11:18433539-18434126	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr11:18433666-18434186	Gliobla	brain:	n/a	n/a
18	TBP	chr11:18433678-18434034	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr11:18433646-18434035	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr11:18433754-18434054	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3A	chr11:18433765-18434009	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr11:18433708-18434043	A549	lung:	n/a	n/a
23	POLR2A	chr11:18433775-18433987	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF1	chr11:18433675-18434157	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr11:18433592-18434135	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr11:18433639-18434122	HEK293	kidney:	n/a	n/a
27	POLR2A	chr11:18433567-18434204	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr11:18433502-18434227	A549	lung:	n/a	n/a
29	GTF2F1	chr11:18433720-18433968	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr11:18433661-18434064	MCF-7	breast:	n/a	n/a
31	CTCF	chr11:18433660-18433810	HBMEC	blood vessel:	n/a	n/a
32	POLR2A	chr11:18433480-18434250	SK-N-MC	brain:	n/a	n/a
33	MAX	chr11:18433626-18434214	H1-hESC	embryonic stem cell:	n/a	n/a
34	EGR1	chr11:18433647-18433849	K562	blood:	n/a	n/a
35	CHD2	chr11:18433576-18433954	H1-hESC	embryonic stem cell:	n/a	n/a
36	E2F6	chr11:18433533-18434363	H1-hESC	embryonic stem cell:	n/a	chr11:18433801-18433810
37	E2F6	chr11:18433672-18434161	H1-hESC	embryonic stem cell:	n/a	chr11:18433801-18433810

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:18433745-18433795	IMR90	lung:	fetal
2	chr11:18433745-18433795	NH-A	brain:	n/a
3	chr11:18433745-18433795	AG04450	lung:	fetal
4	chr11:18433732-18433782	HEEpiC	esophagus:	n/a
5	chr11:18433745-18433795	T-47D	breast:	n/a
6	chr11:18433732-18433782	MCF-7	breast:	n/a
7	chr11:18433732-18433782	PFSK-1	brain:	n/a
8	chr11:18433745-18433795	SK-N-SH	brain:	n/a
9	chr11:18433732-18433782	HNPCEpiC	eye:	n/a
10	chr11:18433745-18433795	HEEpiC	esophagus:	n/a
11	chr11:18433745-18433795	HNPCEpiC	eye:	n/a
12	chr11:18433745-18433795	SAEC	small airway:	n/a
13	chr11:18433732-18433782	HPAEpiC	pulmonary alveolar:	n/a
14	chr11:18433745-18433795	Hela-S3	cervix:	n/a
15	chr11:18433745-18433795	HCF	heart:	n/a
16	chr11:18433732-18433782	HL-60	blood:	n/a
17	chr11:18433732-18433782	IMR90	lung:	fetal
18	chr11:18433745-18433795	ECC-1	luminal epithelium:	n/a
19	chr11:18433732-18433782	HMEC	breast:	n/a
20	chr11:18433745-18433795	GM19239	blood:	n/a
21	chr11:18433732-18433782	LNCaP	prostate:	n/a
22	chr11:18433745-18433795	PANC-1	pancreas:	n/a
23	chr11:18433745-18433795	SK-N-MC	brain:	n/a
24	chr11:18433732-18433782	SK-N-SH	brain:	n/a
25	chr11:18433745-18433795	NT2-D1	testis:	n/a
26	chr11:18433732-18433782	GM06990	blood:	n/a
27	chr11:18433732-18433782	H1-hESC	embryonic stem cell:	embryo
28	chr11:18433745-18433795	PrEC	prostate:	n/a
29	chr11:18433732-18433782	AG09319	gingival:	n/a
30	chr11:18433732-18433782	SK-N-SH_RA	brain:	n/a
31	chr11:18433745-18433795	ovcar-3	ovarian:	n/a
32	chr11:18433745-18433795	A549	lung:	n/a
33	chr11:18433732-18433782	HCPEpiC	choroid plexus:	n/a
34	chr11:18433732-18433782	Jurkat	blood:	n/a
35	chr11:18433732-18433782	HRE	kidney:	n/a
36	chr11:18433745-18433795	HepG2	liver:	n/a
37	chr11:18433745-18433795	HRCEpiC	kidney:	n/a
38	chr11:18433745-18433795	AG09309	skin:	n/a
39	chr11:18433732-18433782	U87	brain:	n/a
40	chr11:18433745-18433795	HCPEpiC	choroid plexus:	n/a
41	chr11:18433732-18433782	NB4	blood:	n/a
42	chr11:18433732-18433782	MCF10A-Er-Src	breast:	n/a
43	chr11:18433732-18433782	HIPEpiC	eye:	n/a
44	chr11:18433732-18433782	HCF	heart:	n/a
45	chr11:18433732-18433782	HCM	heart:	n/a
46	chr11:18433745-18433795	HMEC	breast:	n/a
47	chr11:18433745-18433795	HRE	kidney:	n/a
48	chr11:18433745-18433795	RPTEC	kidney:	n/a
49	chr11:18433745-18433795	PFSK-1	brain:	n/a
50	chr11:18433732-18433782	NT2-D1	testis:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18428578..18433796-chr11:18433952..18441799,12	K562	blood:
2	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:
3	chr11:18416054..18417892-chr11:18432317..18434579,2	K562	blood:
4	chr11:18415873..18420206-chr11:18430045..18435036,6	MCF-7	breast:
5	chr11:18432193..18433875-chr11:18547475..18550164,2	MCF-7	breast:
6	chr11:18423297..18429050-chr11:18429237..18433863,11	K562	blood:

No data

Variant related genes	Relation type
LDHC	TF binding region
LDHC	CpG island
ENSG00000256006	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000134333	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10741744	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10766475	0.96[ASN][1000 genomes]
rs10766478	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10832927	0.89[ASN][1000 genomes]
rs10832929	0.88[ASN][1000 genomes]
rs10832930	0.96[ASN][1000 genomes]
rs10832931	0.96[ASN][1000 genomes]
rs10832932	0.96[ASN][1000 genomes]
rs10832933	0.93[ASN][1000 genomes]
rs1830426	0.94[ASN][1000 genomes]
rs1881716	0.96[ASN][1000 genomes]
rs1969562	0.94[ASN][1000 genomes]
rs1969563	0.94[ASN][1000 genomes]
rs2249631	0.94[ASN][1000 genomes]
rs2403279	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758680	0.96[ASN][1000 genomes]
rs3758682	0.96[ASN][1000 genomes]
rs3781641	0.96[ASN][1000 genomes]
rs3809096	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4274186	0.94[ASN][1000 genomes]
rs5030621	0.96[ASN][1000 genomes]
rs6486421	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486425	0.96[ASN][1000 genomes]
rs7101840	0.83[ASN][1000 genomes]
rs7106099	0.89[ASN][1000 genomes]
rs7111748	0.94[ASN][1000 genomes]
rs7112492	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7117399	0.88[ASN][1000 genomes]
rs7120485	0.94[ASN][1000 genomes]
rs7121244	0.94[ASN][1000 genomes]
rs7128549	0.94[ASN][1000 genomes]
rs7130990	0.94[ASN][1000 genomes]
rs7947664	0.96[ASN][1000 genomes]
rs7951953	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs3809097	LDHC	cis	Skin Sun Exposed Lower leg	GTEx
rs3809097	LDHC	cis	Adipose Subcutaneous	GTEx
rs3809097	LDHC	cis	Whole Blood	GTEx
rs3809097	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs3809097	LDHC	cis	Artery Tibial	GTEx
rs3809097	LDHC	cis	Nerve Tibial	GTEx
rs3809097	LDHC	cis	Thyroid	GTEx
rs3809097	LDHC	cis	Esophagus Muscularis	GTEx
rs3809097	LDHC	cis	Muscle Skeletal	GTEx
rs3809097	LDHC	cis	lung	GTEx

Chromatin state (count:103 , 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	chr11:18422000-18433800	Weak transcription	Stomach Mucosa	stomach
3	chr11:18422200-18433800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:18422600-18433800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:18426400-18433800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:18427200-18433800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr11:18427200-18433800	Weak transcription	Fetal Heart	heart
8	chr11:18427200-18433800	Weak transcription	Small Intestine	intestine
9	chr11:18428000-18433800	Weak transcription	Colonic Mucosa	Colon
10	chr11:18428000-18433800	Weak transcription	Gastric	stomach
11	chr11:18429200-18433800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:18429600-18434200	Weak transcription	HepG2	liver
13	chr11:18430000-18433800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:18430200-18433800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:18430200-18433800	Weak transcription	Brain Substantia Nigra	brain
16	chr11:18430200-18433800	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:18430200-18433800	Weak transcription	HSMMtube	muscle
18	chr11:18430200-18440200	Weak transcription	K562	blood
19	chr11:18430400-18433800	Weak transcription	Brain Angular Gyrus	brain
20	chr11:18430400-18433800	Weak transcription	Pancreas	Pancrea
21	chr11:18430400-18433800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:18430400-18433800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr11:18430400-18433800	Weak transcription	NH-A	brain
24	chr11:18430400-18434200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:18430600-18433800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:18430600-18433800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:18430600-18433800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:18430600-18433800	Weak transcription	Spleen	Spleen
29	chr11:18430600-18434000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr11:18430600-18434000	Weak transcription	Fetal Brain Male	brain
31	chr11:18430800-18433800	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr11:18430800-18433800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:18430800-18433800	Weak transcription	Esophagus	oesophagus
34	chr11:18430800-18433800	Weak transcription	Fetal Stomach	stomach
35	chr11:18430800-18433800	Weak transcription	Lung	lung
36	chr11:18430800-18433800	Weak transcription	Right Ventricle	heart
37	chr11:18430800-18433800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:18430800-18433800	Weak transcription	NHDF-Ad	bronchial
39	chr11:18430800-18434400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:18432800-18434000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr11:18433200-18434000	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr11:18433400-18433800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:18433400-18433800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr11:18433400-18433800	Active TSS	Ovary	ovary
45	chr11:18433400-18434000	Enhancers	HMEC	breast
46	chr11:18433400-18434200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr11:18433400-18434200	Active TSS	Fetal Kidney	kidney
48	chr11:18433400-18434400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
49	chr11:18433400-18434400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:18433400-18434400	Active TSS	Stomach Smooth Muscle	stomach

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