Variant report

Variant	rs1829942
Chromosome Location	chr7:65274674-65274675
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	CUX1	chr7:65274224-65274970	GM12878	blood:	n/a	n/a
2	POLR2A	chr7:65274329-65275056	GM12878	blood:	n/a	n/a
3	BCL3	chr7:65274175-65274895	GM12878	blood:	n/a	n/a
4	FOXM1	chr7:65274037-65275035	GM12878	blood:	n/a	n/a
5	POU2F2	chr7:65274579-65275035	GM12891	blood:	n/a	n/a
6	USF2	chr7:65274326-65275280	GM12878	blood:	n/a	n/a
7	STAT5A	chr7:65274117-65274743	GM12878	blood:	n/a	chr7:65274326-65274335 chr7:65274324-65274338 chr7:65274321-65274341 chr7:65274321-65274341 chr7:65274327-65274336
8	BATF	chr7:65274154-65274674	GM12878	blood:	n/a	chr7:65274424-65274435
9	MTA3	chr7:65274040-65275326	GM12878	blood:	n/a	n/a
10	JUND	chr7:65274003-65275094	GM12878	blood:	n/a	chr7:65274300-65274309
11	MTA3	chr7:65274131-65274763	GM12878	blood:	n/a	n/a
12	BHLHE40	chr7:65274224-65275139	GM12878	blood:	n/a	n/a
13	CHD1	chr7:65274378-65274719	GM12878	blood:	n/a	n/a
14	POLR2A	chr7:65274402-65275254	GM12878	blood:	n/a	n/a
15	NFIC	chr7:65274005-65275263	GM12878	blood:	n/a	chr7:65274289-65274306
16	PAX5	chr7:65274584-65275017	GM12891	blood:	n/a	n/a
17	POU2F2	chr7:65274159-65275138	GM12891	blood:	n/a	chr7:65274211-65274223
18	RCOR1	chr7:65274190-65274698	GM12878	blood:	n/a	n/a
19	SP1	chr7:65274162-65274943	GM12878	blood:	n/a	chr7:65274297-65274318
20	BATF	chr7:65274171-65274675	GM12878	blood:	n/a	chr7:65274424-65274435
21	PAX5	chr7:65274151-65275213	GM12878	blood:	n/a	chr7:65274322-65274332
22	ATF2	chr7:65274089-65274708	GM12878	blood:	n/a	n/a
23	NFATC1	chr7:65274105-65274993	GM12878	blood:	n/a	n/a
24	RELA	chr7:65274199-65275132	GM19099	blood:	n/a	n/a
25	FOXM1	chr7:65274059-65274766	GM12878	blood:	n/a	n/a
26	ZNF384	chr7:65274325-65275135	GM12878	blood:	n/a	n/a
27	NFIC	chr7:65274083-65275016	GM12878	blood:	n/a	chr7:65274289-65274306
28	IRF4	chr7:65274162-65275009	GM12878	blood:	n/a	n/a
29	EP300	chr7:65274197-65275024	GM12878	blood:	n/a	n/a
30	ESRRA	chr7:65274637-65275521	GM12878	blood:	n/a	n/a
31	PML	chr7:65274130-65275112	GM12878	blood:	n/a	n/a
32	MAX	chr7:65274192-65275038	GM12878	blood:	n/a	chr7:65274468-65274477
33	EBF1	chr7:65274184-65275301	GM12878	blood:	n/a	chr7:65274484-65274495 chr7:65274485-65274495 chr7:65274483-65274496
34	NFATC1	chr7:65274089-65274687	GM12878	blood:	n/a	n/a
35	IKZF1	chr7:65274174-65275057	GM12878	blood:	n/a	n/a
36	EBF1	chr7:65274171-65275326	GM12878	blood:	n/a	chr7:65274484-65274495 chr7:65274485-65274495 chr7:65274483-65274496
37	EP300	chr7:65274165-65274942	GM12878	blood:	n/a	n/a
38	EBF1	chr7:65274146-65275342	GM12878	blood:	n/a	chr7:65274484-65274495 chr7:65274485-65274495 chr7:65274483-65274496
39	PAX5	chr7:65274213-65275187	GM12878	blood:	n/a	chr7:65274322-65274332
40	ATF2	chr7:65274055-65275173	GM12878	blood:	n/a	n/a
41	PAX5	chr7:65274155-65275095	GM12878	blood:	n/a	chr7:65274322-65274332
42	RELA	chr7:65274167-65275139	GM18951	blood:	n/a	n/a
43	POLR2A	chr7:65274163-65274757	GM12892	blood:	n/a	n/a
44	TCF12	chr7:65274268-65274759	GM12878	blood:	n/a	n/a
45	MXI1	chr7:65274204-65275151	GM12878	blood:	n/a	n/a
46	POU2F2	chr7:65274179-65275178	GM12878	blood:	n/a	chr7:65274211-65274223
47	RUNX3	chr7:65274092-65275103	GM12878	blood:	n/a	n/a
48	CREB1	chr7:65274153-65274710	GM12878	blood:	n/a	n/a
49	POLR2A	chr7:65274257-65275028	GM12891	blood:	n/a	n/a
50	CREB1	chr7:65274027-65274678	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65273506..65276095-chr7:65278113..65280004,3	K562	blood:

Variant related genes	Relation type
RNU6-912P	TF binding region
ENSG00000200670	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11763003	0.80[EUR][1000 genomes]
rs17711722	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1829943	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517778	chr7:64462326-65326821	ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv429767	chr7:64473713-65415647	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv917231	chr7:64478253-65300317	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1029796	chr7:64494934-65302696	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	esv3339156	chr7:64510176-65349050	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv2759534	chr7:64551274-65373851	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv427788	chr7:64551274-65390424	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
8	esv2764020	chr7:64594065-65351820	Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
9	nsv1018447	chr7:64609892-65308719	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
10	nsv538897	chr7:64609892-65308719	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1029942	chr7:64679680-65371565	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
12	nsv538903	chr7:64679680-65371565	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
13	nsv1019667	chr7:64679680-65380603	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
14	esv2757227	chr7:64694241-65373851	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
15	nsv1025207	chr7:65092426-65339879	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
16	nsv1033400	chr7:65092426-65339879	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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 target site	28 gene(s)	inside rSNPs	diseases
17	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
18	nsv1020622	chr7:65161364-65339879	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1829942	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs1829942	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs1829942	RP4-756H11.3	cis	lung	GTEx
rs1829942	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs1829942	RP4-756H11.3	cis	Thyroid	GTEx
rs1829942	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs1829942	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs1829942	RP4-756H11.3	cis	Artery Tibial	GTEx
rs1829942	RP4-756H11.3	cis	Artery Aorta	GTEx
rs1829942	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65247800-65303400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr7:65260800-65302600	Weak transcription	Gastric	stomach
3	chr7:65263800-65284400	Weak transcription	Spleen	Spleen
4	chr7:65264000-65302600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:65264000-65302800	Weak transcription	Esophagus	oesophagus
6	chr7:65264000-65310800	Weak transcription	Fetal Intestine Small	intestine
7	chr7:65264200-65292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr7:65264600-65292800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:65265600-65304400	Weak transcription	Left Ventricle	heart
10	chr7:65266600-65278800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:65266800-65311000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:65267600-65304000	Weak transcription	Placenta	Placenta
13	chr7:65268400-65279800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:65270200-65282600	Weak transcription	Brain Substantia Nigra	brain
15	chr7:65270200-65286600	Weak transcription	Liver	Liver
16	chr7:65270200-65302800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr7:65273200-65275200	Strong transcription	Pancreas	Pancrea
18	chr7:65273400-65305400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr7:65273800-65277400	Weak transcription	Lung	lung
20	chr7:65273800-65303200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:65274200-65275200	Enhancers	Primary B cells from peripheral blood	blood
22	chr7:65274400-65275600	Flanking Active TSS	GM12878-XiMat	blood
23	chr7:65274600-65275200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:65274600-65275200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:65274600-65283000	Weak transcription	Fetal Intestine Large	intestine
26	chr7:65274600-65303000	Weak transcription	Stomach Smooth Muscle	stomach

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