Variant report

Variant	rs2403279
Chromosome Location	chr11:18416615-18416616
allele	A/C
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	MAX	chr11:18415394-18417156	K562	blood:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
2	POLR2A	chr11:18416613-18417200	GM12891	blood:	n/a	n/a
3	POLR2A	chr11:18415382-18418227	K562	blood:	n/a	n/a
4	POLR2A	chr11:18415374-18419965	PFSK-1	brain:	n/a	n/a
5	SIN3AK20	chr11:18415624-18416709	MCF-7	breast:	n/a	n/a
6	MYC	chr11:18415519-18416804	MCF10A-Er-Src	breast:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
7	UBTF	chr11:18415481-18417943	K562	blood:	n/a	n/a
8	POLR2A	chr11:18415562-18418240	MCF-7	breast:	n/a	n/a
9	HEY1	chr11:18415397-18418254	K562	blood:	n/a	chr11:18416059-18416068 chr11:18416057-18416066
10	MAX	chr11:18415719-18416630	HUVEC	blood vessel:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
11	ELF1	chr11:18415773-18416918	GM12878	blood:	n/a	n/a
12	HA-E2F1	chr11:18415552-18416744	MCF-7	breast:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
13	E2F6	chr11:18415713-18416652	K562	blood:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
14	MYC	chr11:18415324-18418072	Hela-S3	cervix:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
15	MAX	chr11:18415270-18416936	A549	lung:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
16	POLR2A	chr11:18415742-18417294	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:18415572-18418315	GM12878	blood:	n/a	n/a
18	POLR2A	chr11:18415335-18418286	HL-60	blood:	n/a	n/a
19	MAX	chr11:18415310-18418283	HCT-116	colon:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
20	MTA3	chr11:18415294-18418275	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:18415423-18418116	Raji	blood:	n/a	n/a
22	POLR2A	chr11:18415544-18418206	GM18505	blood:	n/a	n/a
23	POLR2A	chr11:18415535-18418317	GM12892	blood:	n/a	n/a
24	POLR2A	chr11:18415500-18418234	HepG2	liver:	n/a	n/a
25	POLR2A	chr11:18415416-18418260	Hela-S3	cervix:	n/a	n/a
26	MAX	chr11:18415440-18417036	H1-hESC	embryonic stem cell:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
27	MAX	chr11:18415509-18418014	Hela-S3	cervix:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
28	POLR2A	chr11:18415356-18422999	PFSK-1	brain:	n/a	n/a
29	E2F6	chr11:18415428-18416638	H1-hESC	embryonic stem cell:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
30	POLR2A	chr11:18415643-18418217	ProgFib	skin:	n/a	n/a
31	CREB1	chr11:18415395-18416632	A549	lung:	n/a	chr11:18416056-18416069
32	PML	chr11:18415457-18418386	GM12878	blood:	n/a	n/a
33	POLR2A	chr11:18415471-18418206	K562	blood:	n/a	n/a
34	HA-E2F1	chr11:18415760-18416639	Hela-S3	cervix:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
35	E2F6	chr11:18415470-18416963	K562	blood:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
36	POLR2A	chr11:18415709-18418162	HepG2	liver:	n/a	n/a
37	POLR2A	chr11:18415788-18416692	HUVEC	blood vessel:	n/a	n/a
38	TAF1	chr11:18415524-18416985	A549	lung:	n/a	n/a
39	POLR2A	chr11:18415433-18418118	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr11:18415529-18418442	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr11:18415527-18417985	MCF10A-Er-Src	breast:	n/a	n/a
42	REST	chr11:18415437-18416642	A549	lung:	n/a	chr11:18415900-18415908
43	MYC	chr11:18415413-18417082	K562	blood:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
44	POLR2A	chr11:18415523-18418309	GM12892	blood:	n/a	n/a
45	SIN3AK20	chr11:18415743-18416931	PANC-1	pancreas:	n/a	n/a
46	E2F6	chr11:18415270-18417024	H1-hESC	embryonic stem cell:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
47	POLR2A	chr11:18415707-18418174	GM18951	blood:	n/a	n/a
48	YY1	chr11:18416303-18416655	GM12878	blood:	n/a	n/a
49	STAT5A	chr11:18415338-18418295	GM12878	blood:	n/a	n/a
50	MXI1	chr11:18415244-18418587	SK-N-SH	brain:	n/a	chr11:18416022-18416031

No.	Distal block	Cell Line	Cell type
1	chr11:18414624..18416918-chr7:148786242..148788890,2	MCF-7	breast:
2	chr11:18340646..18350403-chr11:18414573..18418572,22	K562	blood:
3	chr11:18414795..18417618-chr11:18546727..18549809,4	MCF-7	breast:
4	chr11:18365375..18369096-chr11:18414733..18417585,5	MCF-7	breast:
5	chr11:18415873..18420206-chr11:18430045..18435036,6	MCF-7	breast:
6	chr1:117908068..117910617-chr11:18415187..18418094,2	MCF-7	breast:
7	chr11:18415810..18416651-chr8:67579307..67579955,2	Hela-S3	cervix:
8	chr11:18343053..18346262-chr11:18415665..18418898,6	MCF-7	breast:
9	chr11:18416155..18417729-chr20:42084021..42086862,2	MCF-7	breast:
10	chr11:18415280..18417349-chr11:18656133..18657834,2	MCF-7	breast:
11	chr11:18416054..18417892-chr11:18432317..18434579,2	K562	blood:
12	chr11:18415733..18416650-chr20:62152091..62152621,2	Hela-S3	cervix:
13	chr11:18414231..18417142-chr11:18548434..18550099,2	K562	blood:
14	chr11:18416584..18419436-chr12:7046184..7047780,2	K562	blood:
15	chr11:18340586..18347042-chr11:18413380..18419628,16	K562	blood:
16	chr11:18342491..18345045-chr11:18415566..18419495,5	MCF-7	breast:
17	chr11:18366987..18369152-chr11:18416005..18417921,2	MCF-7	breast:
18	chr11:776928..777866-chr11:18415866..18416625,2	NB4	blood:
19	chr11:18415399..18418482-chr11:18547632..18550708,3	MCF-7	breast:
20	chr11:18415166..18418061-chr11:18653248..18658001,5	K562	blood:
21	chr11:18416044..18417626-chr11:18558294..18561234,2	MCF-7	breast:
22	chr11:18414619..18417567-chr11:18475840..18478644,2	K562	blood:
23	chr11:18415765..18417941-chr11:18547561..18549649,2	K562	blood:
24	chr11:18152566..18154757-chr11:18415660..18417661,2	K562	blood:
25	chr11:18342812..18343809-chr11:18416058..18416846,3	NB4	blood:
26	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:
27	chr11:18415688..18416625-chr12:123236985..123237921,2	NB4	blood:
28	chr1:38455002..38455687-chr11:18415949..18416911,2	HCT-116	colon:
29	chr11:18416119..18416955-chr7:99933156..99933912,2	Hela-S3	cervix:

Variant related genes	Relation type
LDHA	TF binding region
ENSG00000166796	Chromatin interaction
ENSG00000242294	Chromatin interaction
ENSG00000139726	Chromatin interaction
ENSG00000151116	Chromatin interaction
ENSG00000197362	Chromatin interaction
ENSG00000111676	Chromatin interaction
ENSG00000183431	Chromatin interaction
ENSG00000256006	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000272752	Chromatin interaction
ENSG00000166800	Chromatin interaction
ENSG00000124193	Chromatin interaction
ENSG00000270024	Chromatin interaction
ENSG00000175073	Chromatin interaction
ENSG00000125534	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000121716	Chromatin interaction
ENSG00000213865	Chromatin interaction
ENSG00000177225	Chromatin interaction
ENSG00000179826	Chromatin interaction
ENSG00000271427	Chromatin interaction
ENSG00000255284	Chromatin interaction
ENSG00000198162	Chromatin interaction
ENSG00000179119	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 23 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10741744	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10766473	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10766475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10766478	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10832927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10832929	0.91[ASN][1000 genomes]
rs10832930	0.98[ASN][1000 genomes]
rs10832931	0.98[ASN][1000 genomes]
rs10832932	0.98[ASN][1000 genomes]
rs10832933	0.94[ASN][1000 genomes]
rs11024636	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs11024651	0.83[CHB][hapmap]
rs1830426	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1881716	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1881717	0.87[CHB][hapmap]
rs1969562	1.00[ASN][1000 genomes]
rs1969563	1.00[ASN][1000 genomes]
rs2037868	0.83[CHB][hapmap]
rs2249631	1.00[ASN][1000 genomes]
rs2403278	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2658566	0.87[CHB][hapmap]
rs3758680	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3758681	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3758682	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3758683	0.95[JPT][hapmap]
rs3781641	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3809096	0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3809097	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4274186	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4820	0.80[ASN][1000 genomes]
rs5030621	0.98[ASN][1000 genomes]
rs6486421	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486425	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7101840	0.88[ASN][1000 genomes]
rs7106099	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7111748	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7112492	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7117399	0.94[ASN][1000 genomes]
rs7120485	1.00[ASN][1000 genomes]
rs7121244	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7128549	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7129689	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7130990	1.00[ASN][1000 genomes]
rs7947664	0.98[ASN][1000 genomes]
rs7951953	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];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:23)

SNP	Gene	Cis/trans	Tissue	Source
rs2403279	LDHC	cis	Artery Tibial	GTEx
rs2403279	LDHC	cis	Adipose Subcutaneous	GTEx
rs2403279	LDHAL6A	cis	parietal	SCAN
rs2403279	LDHC	cis	Whole Blood	GTEx
rs2403279	LDHC	cis	parietal	SCAN
rs2403279	LDHC	cis	Thyroid	GTEx
rs2403279	LDHC	cis	lung	GTEx
rs2403279	PLEKHA7	cis	parietal	SCAN
rs2403279	LDHC	cis	Nerve Tibial	GTEx
rs2403279	RRAS2	cis	cerebellum	SCAN
rs2403279	TSG101	cis	lymphoblastoid	seeQTL
rs2403279	LDHA	cis	cerebellum	SCAN
rs2403279	LDHC	cis	cerebellum	SCAN
rs2403279	LDHC	cis	Muscle Skeletal	GTEx
rs2403279	LDHC	cis	Esophagus Muscularis	GTEx
rs2403279	COPB1	cis	cerebellum	SCAN
rs2403279	C11orf58	cis	parietal	SCAN
rs2403279	LDHC	cis	uninvolved skin	skin_eQTL
rs2403279	LDHC	cis	multi-tissue	Pritchard
rs2403279	LDHC	cis	lymphoblastoid	seeQTL
rs2403279	LDHAL6A	cis	cerebellum	SCAN
rs2403279	LDHC	cis	Skin Sun Exposed Lower leg	GTEx
rs2403279	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18415400-18416800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:18415400-18416800	Active TSS	Brain Substantia Nigra	brain
3	chr11:18415400-18417600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr11:18415400-18418000	Active TSS	Fetal Kidney	kidney
5	chr11:18415400-18418400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr11:18415600-18416800	Active TSS	Fetal Brain Female	brain
7	chr11:18415600-18417000	Active TSS	Fetal Lung	lung
8	chr11:18415600-18417600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr11:18415600-18418000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr11:18415600-18418000	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr11:18415600-18418200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr11:18415600-18418200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:18415600-18418200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:18415600-18418200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr11:18415600-18418200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr11:18415600-18418400	Active TSS	Psoas Muscle	Psoas
17	chr11:18415800-18417000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr11:18415800-18417000	Active TSS	Stomach Smooth Muscle	stomach
19	chr11:18415800-18417600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:18415800-18417800	Active TSS	Liver	Liver
21	chr11:18415800-18417800	Active TSS	NHEK	skin
22	chr11:18415800-18418000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:18415800-18418000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:18415800-18418000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr11:18415800-18418000	Active TSS	Brain Angular Gyrus	brain
26	chr11:18415800-18418000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr11:18415800-18418000	Active TSS	Left Ventricle	heart
28	chr11:18415800-18418000	Active TSS	Lung	lung
29	chr11:18415800-18418000	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr11:18415800-18418200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr11:18415800-18418200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr11:18415800-18418200	Active TSS	Esophagus	oesophagus
33	chr11:18415800-18418200	Active TSS	Ovary	ovary
34	chr11:18415800-18418400	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr11:18415800-18418400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr11:18415800-18418400	Active TSS	H9 Cell Line	embryonic stem cell
37	chr11:18415800-18418400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr11:18415800-18418400	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr11:18415800-18418400	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr11:18415800-18418400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr11:18415800-18418400	Active TSS	Brain Hippocampus Middle	brain
42	chr11:18415800-18418400	Flanking Active TSS	Placenta	Placenta
43	chr11:18415800-18418400	Active TSS	Small Intestine	intestine
44	chr11:18416000-18416800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:18416000-18416800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr11:18416000-18416800	Active TSS	Primary monocytes fromperipheralblood	blood
47	chr11:18416000-18416800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr11:18416000-18416800	Active TSS	Adipose Nuclei	Adipose
49	chr11:18416000-18416800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr11:18416000-18416800	Active TSS	Skeletal Muscle Male	skeletal muscle

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