Variant report

Variant	rs7112492
Chromosome Location	chr11:18405510-18405511
allele	G/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	NFIC	chr11:18405176-18405972	GM12878	blood:	n/a	n/a
2	MAX	chr11:18405069-18405571	K562	blood:	n/a	n/a
3	TAF1	chr11:18405226-18405700	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr11:18405289-18406349	Hela-S3	cervix:	n/a	n/a
5	JUND	chr11:18405278-18405561	HepG2	liver:	n/a	chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472 chr11:18405461-18405472
6	CUX1	chr11:18405226-18405549	K562	blood:	n/a	n/a
7	STAT3	chr11:18405369-18406152	GM12878	blood:	n/a	chr11:18405909-18405921 chr11:18405830-18405842
8	FOXA2	chr11:18405034-18406287	A549	lung:	n/a	n/a
9	CEBPB	chr11:18405307-18406294	A549	lung:	n/a	n/a
10	SMC3	chr11:18405112-18406290	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:18404744-18406412	HUVEC	blood vessel:	n/a	n/a
12	FOS	chr11:18405089-18406208	HUVEC	blood vessel:	n/a	chr11:18405155-18405164 chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472 chr11:18405461-18405472
13	SP1	chr11:18404488-18406439	A549	lung:	n/a	chr11:18405375-18405385 chr11:18405903-18405916 chr11:18405375-18405385
14	NRF1	chr11:18405462-18405653	GM12878	blood:	n/a	n/a
15	TFAP2A	chr11:18404795-18406386	Hela-S3	cervix:	n/a	chr11:18405463-18405472 chr11:18405553-18405565 chr11:18405553-18405565 chr11:18405553-18405565 chr11:18405553-18405565
16	JUND	chr11:18405091-18406192	A549	lung:	n/a	chr11:18405155-18405164 chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472 chr11:18405461-18405472
17	BATF	chr11:18405254-18405807	GM12878	blood:	n/a	n/a
18	MEF2A	chr11:18405350-18406017	GM12878	blood:	n/a	n/a
19	YY1	chr11:18404998-18405967	A549	lung:	n/a	n/a
20	TCF12	chr11:18405389-18405795	GM12878	blood:	n/a	n/a
21	MXI1	chr11:18405076-18406143	GM12878	blood:	n/a	n/a
22	FOS	chr11:18405107-18406102	MCF10A-Er-Src	breast:	n/a	chr11:18405155-18405164 chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472 chr11:18405461-18405472
23	EP300	chr11:18404996-18406481	A549	lung:	n/a	n/a
24	EP300	chr11:18405178-18405605	SK-N-SH_RA	brain:	n/a	n/a
25	USF1	chr11:18405136-18406279	A549	lung:	n/a	chr11:18406254-18406270
26	MAFK	chr11:18405228-18405552	HepG2	liver:	n/a	chr11:18405498-18405513
27	POLR2A	chr11:18405136-18406311	Hela-S3	cervix:	n/a	n/a
28	FOS	chr11:18405159-18406221	MCF10A-Er-Src	breast:	n/a	chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472 chr11:18405461-18405472
29	POLR2A	chr11:18405099-18406411	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr11:18405063-18406276	GM12892	blood:	n/a	n/a
31	UBTF	chr11:18405265-18406313	K562	blood:	n/a	n/a
32	ZKSCAN1	chr11:18404837-18406170	Hela-S3	cervix:	n/a	n/a
33	REST	chr11:18405012-18406225	PFSK-1	brain:	n/a	chr11:18405236-18405243 chr11:18405824-18405837 chr11:18405820-18405840 chr11:18405821-18405839 chr11:18405820-18405840 chr11:18405033-18405042 chr11:18405822-18405832 chr11:18405820-18405834
34	PML	chr11:18404920-18406242	GM12878	blood:	n/a	chr11:18405464-18405473
35	GTF2B	chr11:18405438-18406017	K562	blood:	n/a	n/a
36	POLR2A	chr11:18405268-18406140	GM12878	blood:	n/a	n/a
37	FOXM1	chr11:18405150-18406291	GM12878	blood:	n/a	n/a
38	JUND	chr11:18405146-18406243	Hela-S3	cervix:	n/a	chr11:18405155-18405164 chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472 chr11:18405461-18405472
39	ZBTB33	chr11:18405111-18406237	A549	lung:	n/a	n/a
40	IKZF1	chr11:18405266-18406172	GM12878	blood:	n/a	n/a
41	FOSL2	chr11:18405042-18406268	A549	lung:	n/a	chr11:18405155-18405164 chr11:18406259-18406268 chr11:18405462-18405472 chr11:18405463-18405471 chr11:18405351-18405362 chr11:18405462-18405472
42	EP300	chr11:18405388-18406094	GM12878	blood:	n/a	n/a
43	SIN3A	chr11:18405501-18405859	GM12878	blood:	n/a	chr11:18405821-18405835 chr11:18405822-18405831
44	KAP1	chr11:18405291-18406172	U2OS	brain:	n/a	chr11:18405464-18405473
45	TAF1	chr11:18405091-18405690	Hela-S3	cervix:	n/a	n/a
46	HEY1	chr11:18405272-18406140	K562	blood:	n/a	n/a
47	TBP	chr11:18405276-18406234	K562	blood:	n/a	n/a
48	ATF2	chr11:18405250-18406175	GM12878	blood:	n/a	n/a
49	BCL3	chr11:18405074-18406342	A549	lung:	n/a	chr11:18405880-18405888
50	MAFK	chr11:18405259-18406064	IMR90	lung:	n/a	chr11:18405498-18405513

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:18405491-18405541	HL-60	blood:	n/a
2	chr11:18405491-18405541	ECC-1	luminal epithelium:	n/a
3	chr11:18405491-18405541	HCT-116	colon:	n/a
4	chr11:18405491-18405541	BE2_C	brain:	n/a
5	chr11:18405491-18405541	HIPEpiC	eye:	n/a
6	chr11:18405491-18405541	HMEC	breast:	n/a
7	chr11:18405491-18405541	HEK293	kidney:	embryo
8	chr11:18405491-18405541	AG04450	lung:	fetal
9	chr11:18405491-18405541	AG10803	skin:	n/a
10	chr11:18405491-18405541	Jurkat	blood:	n/a
11	chr11:18405491-18405541	NT2-D1	testis:	n/a
12	chr11:18405491-18405541	NH-A	brain:	n/a
13	chr11:18405491-18405541	BJ	skin:	n/a
14	chr11:18405491-18405541	ProgFib	skin:	n/a
15	chr11:18405491-18405541	NB4	blood:	n/a
16	chr11:18405491-18405541	HepG2	liver:	n/a
17	chr11:18405491-18405541	AoSMC	blood vessel:	n/a
18	chr11:18405491-18405541	Caco-2	colon:	n/a
19	chr11:18405491-18405541	NHDF-neo	bronchial:	n/a
20	chr11:18405491-18405541	SK-N-SH	brain:	n/a
21	chr11:18405491-18405541	Hela-S3	cervix:	n/a
22	chr11:18405491-18405541	HPAEpiC	pulmonary alveolar:	n/a
23	chr11:18405491-18405541	ovcar-3	ovarian:	n/a
24	chr11:18405491-18405541	SK-N-SH_RA	brain:	n/a
25	chr11:18405491-18405541	AG09319	gingival:	n/a
26	chr11:18405491-18405541	CMK	blood:	n/a
27	chr11:18405491-18405541	K562	blood:	n/a
28	chr11:18405491-18405541	Hepatocyte	liver:	n/a
29	chr11:18405491-18405541	AG04449	skin:	fetal
30	chr11:18405491-18405541	PFSK-1	brain:	n/a
31	chr11:18405491-18405541	GM19239	blood:	n/a
32	chr11:18405491-18405541	U87	brain:	n/a
33	chr11:18405491-18405541	SAEC	small airway:	n/a
34	chr11:18405491-18405541	T-47D	breast:	n/a
35	chr11:18405491-18405541	HRCEpiC	kidney:	n/a
36	chr11:18405491-18405541	HNPCEpiC	eye:	n/a
37	chr11:18405491-18405541	HCM	heart:	n/a
38	chr11:18405491-18405541	SKMC	muscle:	n/a
39	chr11:18405491-18405541	GM12891	blood:	n/a
40	chr11:18405491-18405541	HCPEpiC	choroid plexus:	n/a
41	chr11:18405491-18405541	RPTEC	kidney:	n/a
42	chr11:18405491-18405541	A549	lung:	n/a
43	chr11:18405491-18405541	GM06990	blood:	n/a
44	chr11:18405491-18405541	LNCaP	prostate:	n/a
45	chr11:18405491-18405541	HEEpiC	esophagus:	n/a
46	chr11:18405491-18405541	HRE	kidney:	n/a
47	chr11:18405491-18405541	MCF10A-Er-Src	breast:	n/a
48	chr11:18405491-18405541	NHBE	bronchial:	n/a
49	chr11:18405491-18405541	H1-hESC	embryonic stem cell:	embryo
50	chr11:18405491-18405541	IMR90	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr11:18403635..18406093-chr11:18432067..18434105,2	MCF-7	breast:
2	chr11:18400049..18401686-chr11:18404314..18405882,2	K562	blood:
3	chr11:18404260..18406442-chr11:18407385..18409678,2	MCF-7	breast:
4	chr11:18404463..18406104-chr11:18409610..18411729,2	K562	blood:
5	chr11:18385990..18389914-chr11:18403284..18406325,4	K562	blood:
6	chr11:18343373..18345684-chr11:18403945..18406882,4	MCF-7	breast:
7	chr11:18349981..18351945-chr11:18404895..18407239,2	MCF-7	breast:
8	chr11:18405218..18405915-chr14:23299034..23299589,2	NB4	blood:
9	chr11:18404604..18407545-chr11:18408793..18411812,5	K562	blood:
10	chr11:18405238..18405993-chr9:33817340..33817887,2	Hela-S3	cervix:

Variant related genes	Relation type
MIR3159	TF binding region
MIR3159	CpG island
ENSG00000107341	Chromatin interaction
ENSG00000172590	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000110756	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000264603	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10741744	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10766473	0.86[CHD][hapmap];0.86[JPT][hapmap]
rs10766475	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10766478	0.86[AMR][1000 genomes]
rs10832927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10832929	0.86[ASN][1000 genomes]
rs10832930	0.93[ASN][1000 genomes]
rs10832931	0.93[ASN][1000 genomes]
rs10832932	0.93[ASN][1000 genomes]
rs10832933	0.90[ASN][1000 genomes]
rs11024636	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs1830426	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1881716	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1881717	0.82[CHB][hapmap]
rs1969562	0.96[ASN][1000 genomes]
rs1969563	0.96[ASN][1000 genomes]
rs2249631	0.96[ASN][1000 genomes]
rs2403278	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs2403279	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]
rs2658566	0.82[CHB][hapmap]
rs3758680	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3758681	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs3758682	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3758683	0.95[JPT][hapmap]
rs3781641	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3809096	0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3809097	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4274186	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4756940	0.83[CHB][hapmap]
rs5030621	0.93[ASN][1000 genomes]
rs6486421	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6486425	0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7101840	0.84[ASN][1000 genomes]
rs7106099	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7111748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7117399	0.89[ASN][1000 genomes]
rs7120485	0.96[ASN][1000 genomes]
rs7121244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7128549	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7129689	0.86[CHD][hapmap];0.95[JPT][hapmap]
rs7130990	0.96[ASN][1000 genomes]
rs7947664	0.93[ASN][1000 genomes]
rs7951953	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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	nsv520101	chr11:18401531-18405510	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7112492	LDHC	cis	Adipose Subcutaneous	GTEx
rs7112492	LDHC	cis	Muscle Skeletal	GTEx
rs7112492	LDHC	cis	lung	GTEx
rs7112492	LDHC	cis	uninvolved skin	skin_eQTL
rs7112492	LDHC	cis	Thyroid	GTEx
rs7112492	LDHC	cis	Nerve Tibial	GTEx
rs7112492	LDHC	cis	Artery Tibial	GTEx
rs7112492	LDHC	cis	multi-tissue	Pritchard
rs7112492	LDHC	cis	Skin Sun Exposed Lower leg	GTEx
rs7112492	LDHC	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18403600-18406600	Enhancers	Fetal Intestine Small	intestine
2	chr11:18404200-18405600	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr11:18404200-18405600	Enhancers	Fetal Thymus	thymus
4	chr11:18404200-18406200	Enhancers	Fetal Brain Male	brain
5	chr11:18404200-18406400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr11:18404200-18406400	Enhancers	Fetal Muscle Trunk	muscle
7	chr11:18404200-18406400	Enhancers	Lung	lung
8	chr11:18404200-18406400	Enhancers	HSMMtube	muscle
9	chr11:18404200-18406600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:18404200-18406600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr11:18404200-18406600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:18404200-18406600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:18404200-18406600	Enhancers	Fetal Muscle Leg	muscle
14	chr11:18404200-18406600	Enhancers	Placenta	Placenta
15	chr11:18404200-18406600	Flanking Active TSS	Hela-S3	cervix
16	chr11:18404200-18407000	Enhancers	Fetal Intestine Large	intestine
17	chr11:18404200-18407200	Enhancers	Primary hematopoietic stem cells	blood
18	chr11:18404200-18407200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:18404400-18406200	Enhancers	Fetal Brain Female	brain
20	chr11:18404400-18406400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:18404400-18406400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:18404400-18406400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:18404400-18406400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:18404400-18406400	Enhancers	Brain Angular Gyrus	brain
25	chr11:18404400-18406400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:18404400-18406400	Enhancers	Esophagus	oesophagus
27	chr11:18404400-18406400	Enhancers	Left Ventricle	heart
28	chr11:18404400-18406400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr11:18404400-18406400	Enhancers	Psoas Muscle	Psoas
30	chr11:18404400-18406400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr11:18404400-18406400	Enhancers	Right Ventricle	heart
32	chr11:18404400-18406400	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr11:18404400-18406400	Enhancers	Spleen	Spleen
34	chr11:18404400-18406600	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr11:18404400-18406600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:18404400-18406600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:18404400-18406600	Enhancers	Fetal Heart	heart
38	chr11:18404400-18406600	Enhancers	Fetal Stomach	stomach
39	chr11:18404400-18406600	Enhancers	Small Intestine	intestine
40	chr11:18404400-18406600	Enhancers	Stomach Mucosa	stomach
41	chr11:18404400-18406600	Flanking Active TSS	A549	lung
42	chr11:18404400-18406600	Enhancers	HUVEC	blood vessel
43	chr11:18404400-18407000	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr11:18404400-18407000	Enhancers	Right Atrium	heart
45	chr11:18404400-18407200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:18404400-18407200	Enhancers	Gastric	stomach
47	chr11:18404600-18406200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:18404600-18406200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr11:18404600-18406200	Enhancers	Brain Hippocampus Middle	brain
50	chr11:18404600-18406400	Enhancers	Aorta	Aorta

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