Variant report

Variant	rs4590196
Chromosome Location	chr5:95997285-95997286
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	CEBPB	chr5:95997135-95998154	HCT-116	colon:	n/a	chr5:95997754-95997767 chr5:95997756-95997765 chr5:95997754-95997765
2	POLR2A	chr5:95997074-95999126	GM12892	blood:	n/a	n/a
3	STAT3	chr5:95997169-95997386	MCF10A-Er-Src	breast:	n/a	n/a
4	MTA3	chr5:95997171-95997861	GM12878	blood:	n/a	n/a
5	WRNIP1	chr5:95997114-95997693	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:95997160-95997328	GM12878	blood:	n/a	n/a
7	MAX	chr5:95997246-95999260	GM12878	blood:	n/a	chr5:95998429-95998439
8	SMC3	chr5:95997176-95998021	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr5:95997181-95998869	GM10847	blood:	n/a	n/a
10	TBP	chr5:95997223-95997907	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr5:95996922-95999127	U87	brain:	n/a	n/a
12	POLR2A	chr5:95997088-95999042	GM12892	blood:	n/a	n/a
13	NFIC	chr5:95996986-95997513	GM12878	blood:	n/a	n/a
14	EP300	chr5:95997191-95997339	GM12878	blood:	n/a	n/a
15	POLR2A	chr5:95996990-95997414	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr5:95997205-95999137	PFSK-1	brain:	n/a	n/a
17	SIN3A	chr5:95997094-95999563	H1-hESC	embryonic stem cell:	n/a	chr5:95998255-95998263
18	ATF2	chr5:95997283-95997935	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:95997011-95998992	GM12878	blood:	n/a	n/a
20	POLR2A	chr5:95997181-95998975	GM19193	blood:	n/a	n/a
21	PML	chr5:95996977-95999197	GM12878	blood:	n/a	chr5:95997154-95997162
22	POLR2A	chr5:95997043-95998988	U87	brain:	n/a	n/a
23	NFYB	chr5:95997268-95997336	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:95997103-95997979	GM12878	blood:	n/a	n/a
25	RAD21	chr5:95997243-95997899	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:95996986-95999052	Raji	blood:	n/a	n/a
27	ELF1	chr5:95997037-95999157	GM12878	blood:	n/a	n/a
28	MYC	chr5:95997205-95997371	H1-hESC	embryonic stem cell:	n/a	n/a
29	BHLHE40	chr5:95997232-95998098	GM12878	blood:	n/a	n/a
30	MAZ	chr5:95997255-95997769	K562	blood:	n/a	n/a
31	RELA	chr5:95996828-95998689	GM19099	blood:	n/a	n/a
32	POLR2A	chr5:95997233-95997371	ProgFib	skin:	n/a	n/a
33	SP1	chr5:95996975-95999097	A549	lung:	n/a	chr5:95998653-95998665 chr5:95999036-95999050 chr5:95998674-95998683 chr5:95998654-95998663 chr5:95998673-95998685 chr5:95997976-95997986 chr5:95998321-95998330 chr5:95998673-95998684 chr5:95998674-95998684 chr5:95998654-95998664 chr5:95998675-95998684 chr5:95998674-95998684 chr5:95998674-95998688 chr5:95998653-95998665 chr5:95998673-95998685 chr5:95998650-95998664 chr5:95998654-95998664 chr5:95998655-95998664 chr5:95998404-95998414 chr5:95998655-95998664
34	REST	chr5:95996871-95998155	A549	lung:	n/a	chr5:95997353-95997360 chr5:95998007-95998017
35	POLR2A	chr5:95997216-95999173	IMR90	lung:	n/a	n/a
36	SIN3AK20	chr5:95997131-95997471	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAX	chr5:95997141-95999407	A549	lung:	n/a	chr5:95998429-95998439
38	EP300	chr5:95997149-95998147	A549	lung:	n/a	n/a
39	TCF12	chr5:95996935-95999570	A549	lung:	n/a	n/a
40	EP300	chr5:95997065-95997388	GM12878	blood:	n/a	n/a
41	MAX	chr5:95997075-95999519	Hela-S3	cervix:	n/a	chr5:95998429-95998439
42	POLR2A	chr5:95996266-96000322	Hela-S3	cervix:	n/a	n/a
43	MXI1	chr5:95997136-95999207	GM12878	blood:	n/a	n/a
44	MAX	chr5:95997213-95998121	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr5:95997020-95998988	U87	brain:	n/a	n/a
46	POLR2A	chr5:95997085-95999480	Hela-S3	cervix:	n/a	n/a
47	ZNF384	chr5:95996593-95997882	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:95997048-95999131	GM15510	blood:	n/a	n/a
49	RAD21	chr5:95997087-95997398	IMR90	lung:	n/a	n/a
50	RCOR1	chr5:95997104-95999444	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:95997114..95998690-chr5:96269799..96271534,2	MCF-7	breast:
2	chr5:95997197..95998153-chr6:7541491..7542443,2	Hela-S3	cervix:

Variant related genes	Relation type
CAST	TF binding region
ENSG00000113441	Chromatin interaction
ENSG00000096696	Chromatin interaction
ENSG00000247121	Chromatin interaction
ENSG00000261189	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10045215	0.93[ASN][1000 genomes]
rs10067766	0.95[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10075736	0.93[ASN][1000 genomes]
rs1421911	0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs149319	0.82[YRI][hapmap]
rs151835	1.00[JPT][hapmap]
rs151904	1.00[JPT][hapmap]
rs152005	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs152014	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs152017	0.82[JPT][hapmap]
rs152020	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2351245	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs26482	0.90[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs26483	0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs26484	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs26485	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26503	1.00[JPT][hapmap]
rs26504	1.00[JPT][hapmap]
rs28040	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28093	0.86[JPT][hapmap]
rs28104	0.86[JPT][hapmap]
rs31248	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs31249	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs31250	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4267886	0.93[ASN][1000 genomes]
rs6556937	0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6860934	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6897588	0.95[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7704167	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7705824	0.94[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7733671	0.87[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4590196	CAST	cis	lymphoblastoid	seeQTL
rs4590196	CAST	cis	Whole Blood	GTEx
rs4590196	CAST	cis	lung	GTEx
rs4590196	CAST	cis	multi-tissue	Pritchard
rs4590196	CTC-506B8.1	cis	Nerve Tibial	GTEx
rs4590196	CAST	Cis_1M	lymphoblastoid	RTeQTL
rs4590196	CAST	cis	parietal	SCAN
rs4590196	CTC-506B8.1	cis	Whole Blood	GTEx
rs4590196	CAST	cis	Adipose Subcutaneous	GTEx
rs4590196	CAST	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95992200-95997600	Weak transcription	Gastric	stomach
2	chr5:95996400-95997400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:95996400-95997600	Flanking Active TSS	Hela-S3	cervix
4	chr5:95996400-95997600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr5:95996400-95998000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:95996600-95997400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr5:95996600-95997400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
8	chr5:95996600-95997400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr5:95996600-95997400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr5:95996600-95997400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr5:95996600-95997600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:95996600-95997600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr5:95996600-95997600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
14	chr5:95996600-95997600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:95996600-95997600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr5:95996600-95997600	Flanking Active TSS	NHEK	skin
17	chr5:95996600-95998000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:95996600-95998400	Active TSS	Fetal Brain Female	brain
19	chr5:95996600-95999000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:95996600-95999400	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:95996600-95999400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr5:95996600-95999600	Active TSS	Brain Hippocampus Middle	brain
23	chr5:95996800-95997400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:95996800-95997400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr5:95996800-95997400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:95996800-95997400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:95996800-95997400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:95996800-95997400	Active TSS	HepG2	liver
29	chr5:95996800-95997400	Flanking Active TSS	HUVEC	blood vessel
30	chr5:95996800-95997600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:95996800-95997600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:95996800-95998400	Active TSS	Fetal Stomach	stomach
33	chr5:95996800-95998800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:95996800-95998800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr5:95996800-95999000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr5:95996800-95999000	Active TSS	Duodenum Mucosa	Duodenum
37	chr5:95996800-95999000	Active TSS	Rectal Smooth Muscle	rectum
38	chr5:95996800-95999200	Active TSS	Brain Angular Gyrus	brain
39	chr5:95996800-95999200	Active TSS	Brain Cingulate Gyrus	brain
40	chr5:95996800-95999200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:95996800-95999200	Active TSS	Colonic Mucosa	Colon
42	chr5:95996800-95999200	Active TSS	Colon Smooth Muscle	Colon
43	chr5:95996800-95999200	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr5:95996800-95999200	Active TSS	Left Ventricle	heart
45	chr5:95996800-95999200	Active TSS	Right Ventricle	heart
46	chr5:95996800-95999200	Active TSS	NHDF-Ad	bronchial
47	chr5:95996800-95999400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr5:95996800-95999400	Active TSS	Ovary	ovary
49	chr5:95996800-95999600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:95996800-95999600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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