Variant report

Variant	rs151835
Chromosome Location	chr5:96070982-96070983
allele	A/G
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	JUND	chr5:96070577-96071033	K562	blood:	n/a	n/a
2	TEAD4	chr5:96070540-96071249	ECC-1	luminal epithelium:	n/a	n/a
3	YY1	chr5:96070887-96071050	K562	blood:	n/a	n/a
4	FOS	chr5:96070653-96071135	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr5:96070502-96071010	K562	blood:	n/a	n/a
6	CEBPB	chr5:96070878-96071128	IMR90	lung:	n/a	n/a
7	MAX	chr5:96070602-96071078	K562	blood:	n/a	n/a
8	ATF1	chr5:96070660-96071043	K562	blood:	n/a	n/a
9	FOS	chr5:96070622-96071124	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr5:96070695-96071218	ECC-1	luminal epithelium:	n/a	n/a
11	CEBPB	chr5:96070823-96071161	ECC-1	luminal epithelium:	n/a	n/a
12	GATA3	chr5:96070654-96071571	SK-N-SH	brain:	n/a	chr5:96071164-96071174 chr5:96071076-96071087
13	MYC	chr5:96070663-96071062	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr5:96070875-96071016	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96070439..96072973-chr5:96078050..96080855,3	K562	blood:
2	chr5:95996969..95998528-chr5:96069888..96071858,2	MCF-7	breast:
3	chr5:96068554..96071240-chr5:96073251..96075210,2	K562	blood:
4	chr5:96064043..96066190-chr5:96068496..96071178,2	MCF-7	breast:

Variant related genes	Relation type
CAST	TF binding region
ENSG00000249180	Chromatin interaction
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10067766	1.00[JPT][hapmap]
rs1421911	1.00[JPT][hapmap]
rs149429	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151830	0.96[ASN][1000 genomes]
rs151904	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs152005	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs152014	1.00[JPT][hapmap]
rs152017	0.82[JPT][hapmap]
rs152020	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2351245	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs26482	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs26483	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs26484	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs26485	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs26503	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26504	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28093	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs28104	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs31248	1.00[JPT][hapmap]
rs31249	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs31250	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4590196	1.00[JPT][hapmap]
rs467600	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6556937	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6860934	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6897588	1.00[JPT][hapmap]
rs7704167	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7705824	1.00[JPT][hapmap]
rs7733671	0.84[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv830411	chr5:96045168-96187817	Enhancers Weak transcription Flanking Active TSS Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv516293	chr5:96070205-96216387	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs151835	CAST	cis	Adipose Subcutaneous	GTEx
rs151835	CAST	cis	Whole Blood	GTEx
rs151835	CAST	cis	parietal	SCAN
rs151835	ERAP2	cis	lymphoblastoid	seeQTL
rs151835	C5orf36	cis	cerebellum	SCAN
rs151835	CAST	cis	cerebellum	SCAN
rs151835	CTC-506B8.1	cis	Whole Blood	GTEx
rs151835	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL
rs151835	ERAP1	cis	lung	GTEx
rs151835	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs151835	CTC-506B8.1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96042800-96076200	Weak transcription	GM12878-XiMat	blood
2	chr5:96051000-96073600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:96051200-96076800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:96054800-96077200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr5:96057800-96075200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr5:96057800-96076000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr5:96057800-96098600	Weak transcription	Fetal Brain Male	brain
8	chr5:96058000-96077200	Weak transcription	Small Intestine	intestine
9	chr5:96058000-96078200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr5:96062800-96081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
12	chr5:96064600-96092600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:96065400-96073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:96065800-96073600	Weak transcription	HepG2	liver
15	chr5:96066400-96072600	Weak transcription	Pancreas	Pancrea
16	chr5:96066400-96073200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:96066400-96074400	Weak transcription	Colonic Mucosa	Colon
18	chr5:96066600-96072200	Weak transcription	HUVEC	blood vessel
19	chr5:96066600-96073200	Weak transcription	Brain Hippocampus Middle	brain
20	chr5:96066600-96073200	Weak transcription	HSMMtube	muscle
21	chr5:96066600-96073600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:96066600-96073800	Weak transcription	Fetal Stomach	stomach
23	chr5:96066600-96076000	Weak transcription	Aorta	Aorta
24	chr5:96066600-96076000	Weak transcription	Gastric	stomach
25	chr5:96066600-96076000	Weak transcription	Spleen	Spleen
26	chr5:96066600-96076800	Weak transcription	Fetal Thymus	thymus
27	chr5:96066800-96071800	Weak transcription	Stomach Smooth Muscle	stomach
28	chr5:96066800-96072800	Weak transcription	Brain Anterior Caudate	brain
29	chr5:96066800-96073600	Weak transcription	Brain Angular Gyrus	brain
30	chr5:96066800-96077200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:96066800-96079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:96067000-96071000	Weak transcription	A549	lung
33	chr5:96067000-96071000	Weak transcription	Hela-S3	cervix
34	chr5:96067000-96071200	Weak transcription	HSMM	muscle
35	chr5:96067000-96071800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:96067000-96072000	Weak transcription	Adipose Nuclei	Adipose
37	chr5:96067000-96072000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:96067000-96072800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr5:96067000-96073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr5:96067000-96073200	Weak transcription	Fetal Kidney	kidney
41	chr5:96067000-96073400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:96067000-96073400	Weak transcription	Ovary	ovary
43	chr5:96067000-96073600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:96067000-96073600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:96067000-96073800	Weak transcription	Brain Substantia Nigra	brain
46	chr5:96067200-96072400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:96067200-96072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr5:96067200-96072800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:96067200-96073600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:96067200-96074200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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