Variant report

Variant	rs149313
Chromosome Location	chr5:96070205-96070206
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	CEBPB	chr5:96069600-96070442	HCT-116	colon:	n/a	chr5:96070032-96070043
2	MAX	chr5:96069585-96070231	MCF-7	breast:	n/a	chr5:96070032-96070041 chr5:96070140-96070149
3	ATF3	chr5:96069750-96070296	HCT-116	colon:	n/a	n/a
4	NFIC	chr5:96069559-96070297	ECC-1	luminal epithelium:	n/a	n/a
5	CEBPB	chr5:96069707-96070288	ECC-1	luminal epithelium:	n/a	chr5:96070032-96070043
6	EP300	chr5:96069764-96070214	ECC-1	luminal epithelium:	n/a	chr5:96070141-96070150 chr5:96070140-96070149 chr5:96070029-96070043 chr5:96069895-96069909
7	CEBPB	chr5:96069754-96070221	MCF-7	breast:	n/a	chr5:96070032-96070043
8	SIN3AK20	chr5:96069552-96070416	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr5:96069594-96070274	HCT-116	colon:	n/a	n/a
10	MAX	chr5:96069754-96070213	H1-hESC	embryonic stem cell:	n/a	chr5:96070032-96070041 chr5:96070140-96070149
11	FOSL2	chr5:96069732-96070232	MCF-7	breast:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070141-96070150
12	SIN3AK20	chr5:96069583-96070389	MCF-7	breast:	n/a	n/a
13	SP1	chr5:96069549-96070262	HCT-116	colon:	n/a	chr5:96069660-96069669
14	FOSL1	chr5:96069581-96070385	HCT-116	colon:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070141-96070150
15	POLR2A	chr5:96069843-96070484	Hela-S3	cervix:	n/a	n/a
16	JUN	chr5:96069976-96070287	K562	blood:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070029-96070042 chr5:96070141-96070150
17	RCOR1	chr5:96069871-96070285	K562	blood:	n/a	n/a
18	JUND	chr5:96069640-96070279	MCF-7	breast:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070139-96070150 chr5:96070141-96070149 chr5:96070141-96070150
19	ATF3	chr5:96069825-96070228	K562	blood:	n/a	n/a
20	POLR2A	chr5:96069720-96070225	HCT-116	colon:	n/a	n/a
21	FOS	chr5:96069729-96070298	MCF10A-Er-Src	breast:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070141-96070150
22	TCF7L2	chr5:96069725-96070268	MCF-7	breast:	n/a	chr5:96070140-96070149
23	STAT3	chr5:96069776-96070263	MCF10A-Er-Src	breast:	n/a	chr5:96070141-96070150 chr5:96070140-96070149
24	UBTF	chr5:96070076-96070208	K562	blood:	n/a	n/a
25	JUND	chr5:96069950-96070320	HepG2	liver:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070139-96070150 chr5:96070141-96070149 chr5:96070141-96070150
26	NR2F2	chr5:96069658-96070240	MCF-7	breast:	n/a	n/a
27	FOS	chr5:96069774-96070298	MCF10A-Er-Src	breast:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070141-96070150
28	JUND	chr5:96069621-96070381	HCT-116	colon:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070139-96070150 chr5:96070141-96070149 chr5:96070141-96070150
29	CEBPB	chr5:96069941-96070206	HepG2	liver:	n/a	chr5:96070032-96070043
30	GATA3	chr5:96069596-96070325	MCF-7	breast:	n/a	chr5:96069897-96069907
31	CEBPB	chr5:96069872-96070218	K562	blood:	n/a	chr5:96070032-96070043
32	FOS	chr5:96069784-96070298	MCF10A-Er-Src	breast:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070141-96070150
33	MAX	chr5:96069589-96070272	ECC-1	luminal epithelium:	n/a	chr5:96070032-96070041 chr5:96070140-96070149
34	JUND	chr5:96069887-96070325	K562	blood:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070139-96070150 chr5:96070141-96070149 chr5:96070141-96070150
35	ZNF217	chr5:96069718-96070221	MCF-7	breast:	n/a	n/a
36	SP1	chr5:96069583-96070298	HCT-116	colon:	n/a	chr5:96069660-96069669
37	TCF12	chr5:96069631-96070295	ECC-1	luminal epithelium:	n/a	n/a
38	CEBPB	chr5:96069610-96070330	HCT-116	colon:	n/a	chr5:96070032-96070043
39	CEBPB	chr5:96069852-96070229	K562	blood:	n/a	chr5:96070032-96070043
40	MAX	chr5:96069638-96070246	MCF-7	breast:	n/a	chr5:96070032-96070041 chr5:96070140-96070149
41	GATA3	chr5:96069665-96070213	T-47D	breast:	n/a	chr5:96069897-96069907
42	FOXM1	chr5:96069567-96070395	ECC-1	luminal epithelium:	n/a	n/a
43	EP300	chr5:96069464-96070377	ECC-1	luminal epithelium:	n/a	chr5:96070141-96070150 chr5:96070140-96070149 chr5:96070029-96070043 chr5:96069895-96069909
44	ATF1	chr5:96069895-96070237	K562	blood:	n/a	n/a
45	GATA3	chr5:96069500-96070358	MCF-7	breast:	n/a	chr5:96069897-96069907
46	FOS	chr5:96069847-96070285	MCF10A-Er-Src	breast:	n/a	chr5:96070142-96070149 chr5:96070140-96070149 chr5:96070141-96070149 chr5:96070141-96070150
47	CEBPB	chr5:96069667-96070227	ECC-1	luminal epithelium:	n/a	chr5:96070032-96070043
48	MAX	chr5:96069604-96070260	ECC-1	luminal epithelium:	n/a	chr5:96070032-96070041 chr5:96070140-96070149
49	CEBPB	chr5:96069696-96070394	MCF-7	breast:	n/a	chr5:96070032-96070043
50	TCF12	chr5:96069528-96070384	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96067837..96070454-chr5:96104057..96106955,2	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
ENSG00000153113	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs149319	0.86[JPT][hapmap]
rs151828	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151829	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs151830	0.80[EUR][1000 genomes]
rs26506	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs26515	0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs27852	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs697976	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314177	0.80[ASN][1000 genomes]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs149313	GPR150	cis	cerebellum	SCAN
rs149313	CAST	cis	parietal	SCAN
rs149313	ELL2	cis	cerebellum	SCAN
rs149313	ARTS-1	cis	multi-tissue	Pritchard
rs149313	ARTS-1	Cis_1M	lymphoblastoid	RTeQTL

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	chr5:96062200-96070800	Weak transcription	Fetal Lung	lung
11	chr5:96062800-96081400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:96063000-96126200	Weak transcription	Brain Germinal Matrix	brain
13	chr5:96064600-96092600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:96065400-96073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:96065800-96073600	Weak transcription	HepG2	liver
16	chr5:96066400-96072600	Weak transcription	Pancreas	Pancrea
17	chr5:96066400-96073200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:96066400-96074400	Weak transcription	Colonic Mucosa	Colon
19	chr5:96066600-96072200	Weak transcription	HUVEC	blood vessel
20	chr5:96066600-96073200	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:96066600-96073200	Weak transcription	HSMMtube	muscle
22	chr5:96066600-96073600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:96066600-96073800	Weak transcription	Fetal Stomach	stomach
24	chr5:96066600-96076000	Weak transcription	Aorta	Aorta
25	chr5:96066600-96076000	Weak transcription	Gastric	stomach
26	chr5:96066600-96076000	Weak transcription	Spleen	Spleen
27	chr5:96066600-96076800	Weak transcription	Fetal Thymus	thymus
28	chr5:96066800-96071800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr5:96066800-96072800	Weak transcription	Brain Anterior Caudate	brain
30	chr5:96066800-96073600	Weak transcription	Brain Angular Gyrus	brain
31	chr5:96066800-96077200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr5:96066800-96079400	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr5:96067000-96071000	Weak transcription	A549	lung
34	chr5:96067000-96071000	Weak transcription	Hela-S3	cervix
35	chr5:96067000-96071200	Weak transcription	HSMM	muscle
36	chr5:96067000-96071800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:96067000-96072000	Weak transcription	Adipose Nuclei	Adipose
38	chr5:96067000-96072000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr5:96067000-96072800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr5:96067000-96073000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:96067000-96073200	Weak transcription	Fetal Kidney	kidney
42	chr5:96067000-96073400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr5:96067000-96073400	Weak transcription	Ovary	ovary
44	chr5:96067000-96073600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr5:96067000-96073600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr5:96067000-96073800	Weak transcription	Brain Substantia Nigra	brain
47	chr5:96067200-96070400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:96067200-96072400	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr5:96067200-96072800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:96067200-96072800	Weak transcription	Fetal Muscle Trunk	muscle

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