Variant report

Variant	rs156835
Chromosome Location	chr5:53345795-53345796
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	NFIC	chr5:53345594-53346194	SK-N-SH	brain:	n/a	n/a
2	TCF12	chr5:53345626-53346192	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr5:53345782-53346092	SK-N-SH	brain:	n/a	n/a
4	EP300	chr5:53345612-53346356	A549	lung:	n/a	chr5:53345879-53345893
5	GATA3	chr5:53345584-53346271	SK-N-SH	brain:	n/a	n/a
6	CEBPB	chr5:53345702-53346217	A549	lung:	n/a	chr5:53346171-53346179
7	MAX	chr5:53345649-53346190	A549	lung:	n/a	n/a
8	SP1	chr5:53345648-53346339	A549	lung:	n/a	n/a
9	MAX	chr5:53345564-53346267	A549	lung:	n/a	n/a
10	FOXA2	chr5:53345749-53346269	A549	lung:	n/a	n/a
11	SP1	chr5:53345595-53346280	A549	lung:	n/a	n/a
12	TCF12	chr5:53345475-53346375	A549	lung:	n/a	n/a
13	EP300	chr5:53345611-53346373	A549	lung:	n/a	chr5:53345879-53345893
14	GATA3	chr5:53345655-53346368	A549	lung:	n/a	n/a
15	PBX3	chr5:53345772-53346276	SK-N-SH	brain:	n/a	n/a
16	PBX3	chr5:53345686-53346141	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RN7SL801P	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs156381	0.81[JPT][hapmap]
rs156382	0.80[JPT][hapmap]
rs156389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156441	0.81[JPT][hapmap]
rs156443	0.81[JPT][hapmap]
rs156822	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs156823	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs156829	0.89[CEU][hapmap];0.81[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs156837	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156839	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs156840	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs255766	0.81[JPT][hapmap]
rs273219	0.81[JPT][hapmap]
rs273220	0.81[JPT][hapmap]
rs274373	0.81[JPT][hapmap]
rs696195	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs696196	0.83[AMR][1000 genomes]
rs696197	0.95[CHB][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs696199	0.95[CHB][hapmap]
rs697098	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs697104	0.82[AMR][1000 genomes]
rs697105	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs697110	0.95[CHB][hapmap]
rs717513	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv881265	chr5:53305742-53504764	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
7	nsv880619	chr5:53305742-53525671	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv881616	chr5:53305742-53639975	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv881018	chr5:53305742-53744849	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv880734	chr5:53305742-53770217	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv881161	chr5:53305742-53815495	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
12	nsv881600	chr5:53305742-53823285	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS 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	16 gene(s)	inside rSNPs	diseases
13	nsv598176	chr5:53311502-53739530	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv880773	chr5:53311918-53815495	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1024303	chr5:53317896-53788276	Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
16	nsv1029224	chr5:53317896-53812899	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
17	nsv949098	chr5:53317990-53816782	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
18	nsv1020517	chr5:53324930-53759046	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
19	nsv1015340	chr5:53326385-53471882	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1017768	chr5:53326385-53752165	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
21	nsv1032352	chr5:53327170-53762973	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
22	nsv598177	chr5:53333477-53755208	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs156835	NDUFS4	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53316200-53387400	Weak transcription	Left Ventricle	heart
2	chr5:53328200-53351600	Weak transcription	Primary T cells from cord blood	blood
3	chr5:53337400-53359200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:53337400-53366400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr5:53340400-53359000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:53341600-53359200	Weak transcription	Right Ventricle	heart
7	chr5:53341800-53356200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:53341800-53364400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:53343000-53351400	Weak transcription	Fetal Intestine Small	intestine
10	chr5:53343000-53368000	Weak transcription	Pancreas	Pancrea
11	chr5:53343600-53376400	Weak transcription	K562	blood
12	chr5:53344600-53345800	Enhancers	NHDF-Ad	bronchial
13	chr5:53344600-53346400	Enhancers	HSMMtube	muscle
14	chr5:53344800-53345800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:53344800-53345800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:53344800-53345800	Enhancers	Fetal Heart	heart
17	chr5:53345000-53346000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr5:53345000-53346400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:53345000-53346600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:53345000-53346600	Enhancers	NHLF	lung
21	chr5:53345200-53346200	Enhancers	Osteobl	bone
22	chr5:53345400-53346000	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr5:53345400-53347200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:53345600-53346000	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr5:53345600-53346000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr5:53345600-53346200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr5:53345600-53346400	Enhancers	Fetal Stomach	stomach
28	chr5:53345600-53346600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr5:53345600-53347200	Flanking Active TSS	A549	lung

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