Variant report

Variant	rs2249631
Chromosome Location	chr11:18416868-18416869
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	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	RAD21	chr11:18416827-18418032	IMR90	lung:	n/a	n/a
6	UBTF	chr11:18415481-18417943	K562	blood:	n/a	n/a
7	POLR2A	chr11:18415562-18418240	MCF-7	breast:	n/a	n/a
8	HEY1	chr11:18415397-18418254	K562	blood:	n/a	chr11:18416059-18416068 chr11:18416057-18416066
9	ELF1	chr11:18415773-18416918	GM12878	blood:	n/a	n/a
10	MYC	chr11:18415324-18418072	Hela-S3	cervix:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
11	MAX	chr11:18415270-18416936	A549	lung:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
12	POLR2A	chr11:18415742-18417294	GM12878	blood:	n/a	n/a
13	POLR2A	chr11:18415572-18418315	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:18415335-18418286	HL-60	blood:	n/a	n/a
15	MAX	chr11:18415310-18418283	HCT-116	colon:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
16	MTA3	chr11:18415294-18418275	GM12878	blood:	n/a	n/a
17	POLR2A	chr11:18415423-18418116	Raji	blood:	n/a	n/a
18	POLR2A	chr11:18415544-18418206	GM18505	blood:	n/a	n/a
19	POLR2A	chr11:18415535-18418317	GM12892	blood:	n/a	n/a
20	POLR2A	chr11:18415500-18418234	HepG2	liver:	n/a	n/a
21	SIN3AK20	chr11:18416747-18418219	MCF-7	breast:	n/a	n/a
22	POLR2A	chr11:18415416-18418260	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr11:18416625-18416963	A549	lung:	n/a	n/a
24	MAX	chr11:18415440-18417036	H1-hESC	embryonic stem cell:	n/a	chr11:18415924-18415931 chr11:18415923-18415932
25	MAX	chr11:18415509-18418014	Hela-S3	cervix:	n/a	chr11:18417082-18417092 chr11:18415924-18415931 chr11:18415923-18415932
26	POLR2A	chr11:18415356-18422999	PFSK-1	brain:	n/a	n/a
27	POLR2A	chr11:18416728-18417229	HepG2	liver:	n/a	n/a
28	REST	chr11:18416624-18416975	A549	lung:	n/a	n/a
29	POLR2A	chr11:18415643-18418217	ProgFib	skin:	n/a	n/a
30	POLR2A	chr11:18416853-18418145	A549	lung:	n/a	n/a
31	PML	chr11:18415457-18418386	GM12878	blood:	n/a	n/a
32	POLR2A	chr11:18415471-18418206	K562	blood:	n/a	n/a
33	E2F6	chr11:18415470-18416963	K562	blood:	n/a	chr11:18416059-18416068 chr11:18416087-18416102 chr11:18416057-18416066 chr11:18416089-18416101
34	POLR2A	chr11:18415709-18418162	HepG2	liver:	n/a	n/a
35	TAF1	chr11:18415524-18416985	A549	lung:	n/a	n/a
36	TAF1	chr11:18416714-18418100	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr11:18416728-18418161	K562	blood:	n/a	n/a
38	RCOR1	chr11:18416644-18416998	Hela-S3	cervix:	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	RELA	chr11:18416667-18418143	GM15510	blood:	n/a	n/a
42	POLR2A	chr11:18415527-18417985	MCF10A-Er-Src	breast:	n/a	n/a
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	STAT5A	chr11:18415338-18418295	GM12878	blood:	n/a	n/a
49	MXI1	chr11:18415244-18418587	SK-N-SH	brain:	n/a	chr11:18416022-18416031
50	POLR2A	chr11:18415479-18418217	Hela-S3	cervix:	n/a	n/a

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	chr11:18343053..18346262-chr11:18415665..18418898,6	MCF-7	breast:
8	chr11:18416155..18417729-chr20:42084021..42086862,2	MCF-7	breast:
9	chr11:18415280..18417349-chr11:18656133..18657834,2	MCF-7	breast:
10	chr11:18416054..18417892-chr11:18432317..18434579,2	K562	blood:
11	chr11:18414231..18417142-chr11:18548434..18550099,2	K562	blood:
12	chr11:18416584..18419436-chr12:7046184..7047780,2	K562	blood:
13	chr11:18340586..18347042-chr11:18413380..18419628,16	K562	blood:
14	chr11:18342491..18345045-chr11:18415566..18419495,5	MCF-7	breast:
15	chr11:18366987..18369152-chr11:18416005..18417921,2	MCF-7	breast:
16	chr11:18415399..18418482-chr11:18547632..18550708,3	MCF-7	breast:
17	chr11:18415166..18418061-chr11:18653248..18658001,5	K562	blood:
18	chr11:18416044..18417626-chr11:18558294..18561234,2	MCF-7	breast:
19	chr11:18414619..18417567-chr11:18475840..18478644,2	K562	blood:
20	chr11:18415765..18417941-chr11:18547561..18549649,2	K562	blood:
21	chr11:18152566..18154757-chr11:18415660..18417661,2	K562	blood:
22	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:
23	chr1:38455002..38455687-chr11:18415949..18416911,2	HCT-116	colon:
24	chr11:18416119..18416955-chr7:99933156..99933912,2	Hela-S3	cervix:

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

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10741744	0.91[ASN][1000 genomes]
rs10766475	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766478	0.82[ASN][1000 genomes]
rs10832927	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10832929	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832931	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832932	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10832933	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1830426	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881716	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969562	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969563	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2403279	1.00[ASN][1000 genomes]
rs2721123	0.88[AMR][1000 genomes]
rs3758680	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758682	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3781641	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809096	0.90[ASN][1000 genomes]
rs3809097	0.94[ASN][1000 genomes]
rs4274186	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs5030621	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486421	1.00[ASN][1000 genomes]
rs6486425	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7101840	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7106099	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7111748	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112492	0.96[ASN][1000 genomes]
rs7117399	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7120485	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121244	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128549	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7130990	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947664	0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2249631	LDHC	cis	Nerve Tibial	GTEx
rs2249631	LDHC	cis	Artery Tibial	GTEx
rs2249631	LDHC	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18415400-18417600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr11:18415400-18418000	Active TSS	Fetal Kidney	kidney
3	chr11:18415400-18418400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:18415600-18417000	Active TSS	Fetal Lung	lung
5	chr11:18415600-18417600	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr11:18415600-18418000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:18415600-18418000	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr11:18415600-18418200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:18415600-18418200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:18415600-18418200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:18415600-18418200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr11:18415600-18418200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:18415600-18418400	Active TSS	Psoas Muscle	Psoas
14	chr11:18415800-18417000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
15	chr11:18415800-18417000	Active TSS	Stomach Smooth Muscle	stomach
16	chr11:18415800-18417600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:18415800-18417800	Active TSS	Liver	Liver
18	chr11:18415800-18417800	Active TSS	NHEK	skin
19	chr11:18415800-18418000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:18415800-18418000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:18415800-18418000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:18415800-18418000	Active TSS	Brain Angular Gyrus	brain
23	chr11:18415800-18418000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr11:18415800-18418000	Active TSS	Left Ventricle	heart
25	chr11:18415800-18418000	Active TSS	Lung	lung
26	chr11:18415800-18418000	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr11:18415800-18418200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr11:18415800-18418200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr11:18415800-18418200	Active TSS	Esophagus	oesophagus
30	chr11:18415800-18418200	Active TSS	Ovary	ovary
31	chr11:18415800-18418400	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr11:18415800-18418400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr11:18415800-18418400	Active TSS	H9 Cell Line	embryonic stem cell
34	chr11:18415800-18418400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:18415800-18418400	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr11:18415800-18418400	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr11:18415800-18418400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr11:18415800-18418400	Active TSS	Brain Hippocampus Middle	brain
39	chr11:18415800-18418400	Flanking Active TSS	Placenta	Placenta
40	chr11:18415800-18418400	Active TSS	Small Intestine	intestine
41	chr11:18416000-18417000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr11:18416000-18417000	Active TSS	Primary B cells from peripheral blood	blood
43	chr11:18416000-18417000	Active TSS	Duodenum Mucosa	Duodenum
44	chr11:18416000-18417000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr11:18416000-18417000	Active TSS	Fetal Muscle Leg	muscle
46	chr11:18416000-18417000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr11:18416000-18417000	Active TSS	HUVEC	blood vessel
48	chr11:18416000-18417200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:18416000-18417200	Active TSS	Fetal Heart	heart
50	chr11:18416000-18417800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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