Variant report

Variant	rs7947664
Chromosome Location	chr11:18426138-18426139
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:18425581-18426150	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:18423186-18426169	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr11:18424754-18426640	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:18425447-18426162	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
6	POLR2A	chr11:18425621-18426138	K562	blood:	n/a	n/a
7	POLR2A	chr11:18423654-18428119	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr11:18423799-18427360	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:18414611..18420404-chr11:18425224..18433817,11	K562	blood:
2	chr11:18342292..18344024-chr11:18424254..18426618,2	MCF-7	breast:
3	chr11:18423297..18429050-chr11:18429237..18433863,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000256006	TF binding region
ENSG00000134333	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000110768	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10741744	0.89[ASN][1000 genomes]
rs10766475	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10766478	0.84[ASN][1000 genomes]
rs10832927	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10832929	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832931	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832932	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832933	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1830426	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1881716	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1969562	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1969563	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2249631	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403279	0.98[ASN][1000 genomes]
rs2721123	0.83[AMR][1000 genomes]
rs3758680	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3758682	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3781641	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809096	0.92[ASN][1000 genomes]
rs3809097	0.96[ASN][1000 genomes]
rs4274186	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820	0.82[ASN][1000 genomes]
rs5030621	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486421	0.98[ASN][1000 genomes]
rs6486425	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7101840	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7106099	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7111748	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7112492	0.93[ASN][1000 genomes]
rs7117399	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120485	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7121244	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7128549	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7130990	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7951953	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv39368	chr11:18425698-18426354	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7947664	LDHC	cis	Thyroid	GTEx
rs7947664	LDHC	cis	Artery 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	chr11:18418600-18427800	Strong transcription	Liver	Liver
7	chr11:18418600-18428600	Strong transcription	Fetal Intestine Large	intestine
8	chr11:18418600-18429400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:18418600-18429800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr11:18418600-18430400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr11:18418600-18430400	Strong transcription	Primary B cells from peripheral blood	blood
12	chr11:18418600-18430400	Strong transcription	Placenta	Placenta
13	chr11:18418600-18430400	Strong transcription	Rectal Mucosa Donor 31	rectum
14	chr11:18418600-18430400	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr11:18418600-18430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:18418600-18430600	Strong transcription	Placenta Amnion	Placenta Amnion
17	chr11:18418600-18430600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr11:18418600-18430800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:18418600-18430800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr11:18418600-18430800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:18418600-18430800	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:18418600-18430800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr11:18418600-18430800	Strong transcription	Fetal Muscle Leg	muscle
24	chr11:18418600-18430800	Strong transcription	Fetal Stomach	stomach
25	chr11:18418600-18430800	Strong transcription	Fetal Thymus	thymus
26	chr11:18418600-18430800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr11:18418600-18430800	Strong transcription	Right Ventricle	heart
28	chr11:18418800-18427400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr11:18418800-18427600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:18418800-18430400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:18418800-18430600	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr11:18418800-18430600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr11:18418800-18430600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:18418800-18430600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:18418800-18430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr11:18418800-18430800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:18418800-18430800	Strong transcription	Adipose Nuclei	Adipose
38	chr11:18418800-18430800	Strong transcription	Osteobl	bone
39	chr11:18418800-18431000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr11:18419000-18426800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:18419000-18428000	Strong transcription	Colonic Mucosa	Colon
42	chr11:18419000-18429200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:18419000-18430000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:18419000-18430400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:18419000-18430600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr11:18419000-18430800	Strong transcription	Brain Anterior Caudate	brain
47	chr11:18419000-18430800	Strong transcription	Fetal Intestine Small	intestine
48	chr11:18419000-18431400	Strong transcription	HSMM	muscle
49	chr11:18419200-18428400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:18419200-18430400	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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