Variant report

Variant	rs1881716
Chromosome Location	chr11:18425018-18425019
allele	C/T
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	POLR2A	chr11:18423152-18426137	U87	brain:	n/a	n/a
2	POLR2A	chr11:18423172-18426105	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:18423186-18426169	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr11:18423656-18426137	U87	brain:	n/a	n/a
5	POLR2A	chr11:18424754-18426640	HepG2	liver:	n/a	n/a
6	POLR2A	chr11:18415270-18432749	U87	brain:	n/a	n/a
7	POLR2A	chr11:18423654-18428119	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr11:18423152-18426131	HepG2	liver:	n/a	n/a
9	POLR2A	chr11:18423307-18425413	K562	blood:	n/a	n/a
10	POLR2A	chr11:18423799-18427360	HepG2	liver:	n/a	n/a
11	POLR2A	chr11:18424809-18426115	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr11:18415373-18432749	U87	brain:	n/a	n/a

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

Variant related genes	Relation type
ENSG00000256006	TF binding region
ENSG00000110768	Chromatin interaction
ENSG00000110756	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];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[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];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832929	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10832930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10832933	0.98[AFR][1000 genomes];1.00[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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1881717	0.87[CHB][hapmap]
rs1969562	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969563	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037868	0.83[CHB][hapmap]
rs2249631	0.97[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	0.85[AMR][1000 genomes]
rs3758680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3758681	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3758682	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]
rs3758683	0.95[JPT][hapmap]
rs3781641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs5030621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486421	0.97[ASN][1000 genomes]
rs6486425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7101840	0.91[AFR][1000 genomes];0.89[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];0.95[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];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[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	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7120485	0.94[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7129689	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7130990	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7947664	0.87[AFR][1000 genomes];0.94[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
rs1881716	TSG101	cis	lymphoblastoid	seeQTL
rs1881716	LDHC	cis	cerebellum	SCAN
rs1881716	LDHC	cis	parietal	SCAN
rs1881716	COPB1	cis	cerebellum	SCAN
rs1881716	LDHAL6A	cis	cerebellum	SCAN
rs1881716	LDHC	cis	Artery Tibial	GTEx
rs1881716	LDHC	cis	multi-tissue	Pritchard
rs1881716	PLEKHA7	cis	parietal	SCAN
rs1881716	LDHC	cis	Thyroid	GTEx
rs1881716	LDHA	cis	lymphoblastoid	GTEx
rs1881716	C11orf58	cis	parietal	SCAN
rs1881716	LDHAL6A	cis	parietal	SCAN
rs1881716	LDHC	cis	lymphoblastoid	seeQTL
rs1881716	LDHA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18418200-18425600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18418200-18433800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18418400-18430600	Strong transcription	Fetal Muscle Trunk	muscle
4	chr11:18418400-18430800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:18418400-18430800	Strong transcription	Left Ventricle	heart
6	chr11:18418400-18433200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:18418600-18427800	Strong transcription	Liver	Liver
8	chr11:18418600-18428600	Strong transcription	Fetal Intestine Large	intestine
9	chr11:18418600-18429400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:18418600-18429800	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr11:18418600-18430400	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr11:18418600-18430400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr11:18418600-18430400	Strong transcription	Placenta	Placenta
14	chr11:18418600-18430400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr11:18418600-18430400	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:18418600-18430600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:18418600-18430600	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr11:18418600-18430600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr11:18418600-18430800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:18418600-18430800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr11:18418600-18430800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr11:18418600-18430800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr11:18418600-18430800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:18418600-18430800	Strong transcription	Fetal Muscle Leg	muscle
25	chr11:18418600-18430800	Strong transcription	Fetal Stomach	stomach
26	chr11:18418600-18430800	Strong transcription	Fetal Thymus	thymus
27	chr11:18418600-18430800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr11:18418600-18430800	Strong transcription	Right Ventricle	heart
29	chr11:18418800-18427400	Strong transcription	Primary hematopoietic stem cells	blood
30	chr11:18418800-18427600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:18418800-18430400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:18418800-18430600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr11:18418800-18430600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr11:18418800-18430600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:18418800-18430600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:18418800-18430800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:18418800-18430800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:18418800-18430800	Strong transcription	Adipose Nuclei	Adipose
39	chr11:18418800-18430800	Strong transcription	Osteobl	bone
40	chr11:18418800-18431000	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr11:18419000-18426800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:18419000-18428000	Strong transcription	Colonic Mucosa	Colon
43	chr11:18419000-18429200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:18419000-18430000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr11:18419000-18430400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:18419000-18430600	Strong transcription	Duodenum Mucosa	Duodenum
47	chr11:18419000-18430800	Strong transcription	Brain Anterior Caudate	brain
48	chr11:18419000-18430800	Strong transcription	Fetal Intestine Small	intestine
49	chr11:18419000-18431400	Strong transcription	HSMM	muscle
50	chr11:18419200-18428400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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