Variant report

Variant	rs973589
Chromosome Location	chr5:114506461-114506462
allele	A/C
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	MAX	chr5:114504989-114506587	A549	lung:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
2	NRF1	chr5:114505143-114506569	SK-N-SH	brain:	n/a	chr5:114506184-114506193
3	CTBP2	chr5:114504745-114506603	H1-hESC	embryonic stem cell:	n/a	n/a
4	HA-E2F1	chr5:114504600-114507035	MCF-7	breast:	n/a	chr5:114505148-114505160 chr5:114505940-114505950 chr5:114506565-114506579 chr5:114506232-114506242 chr5:114506184-114506193
5	E2F6	chr5:114504890-114506654	H1-hESC	embryonic stem cell:	n/a	chr5:114505148-114505160 chr5:114505940-114505950 chr5:114506565-114506579 chr5:114506232-114506242 chr5:114506184-114506193
6	MAX	chr5:114505049-114506763	MCF-7	breast:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
7	MYC	chr5:114504929-114506946	NB4	blood:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
8	MXI1	chr5:114504717-114506647	IMR90	lung:	n/a	chr5:114505673-114505688 chr5:114505675-114505690
9	MAX	chr5:114504810-114506590	H1-hESC	embryonic stem cell:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
10	TAF1	chr5:114504729-114506578	ECC-1	luminal epithelium:	n/a	n/a
11	ZBTB7A	chr5:114504758-114506729	ECC-1	luminal epithelium:	n/a	n/a
12	CCNT2	chr5:114505236-114506493	K562	blood:	n/a	n/a
13	TCF7L2	chr5:114504815-114506517	HCT-116	colon:	n/a	n/a
14	POLR2A	chr5:114504748-114506591	H1-neurons	neurons:	n/a	n/a
15	SIN3A	chr5:114504585-114506905	H1-hESC	embryonic stem cell:	n/a	chr5:114505565-114505576 chr5:114505804-114505815
16	POLR2A	chr5:114505167-114506968	SK-N-MC	brain:	n/a	n/a
17	MAX	chr5:114504568-114506581	HCT-116	colon:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
18	MAX	chr5:114504638-114506607	ECC-1	luminal epithelium:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
19	CTCF	chr5:114504714-114506485	SK-N-SH	brain:	n/a	n/a
20	REST	chr5:114506332-114506535	H1-hESC	embryonic stem cell:	n/a	chr5:114506374-114506392
21	ZBTB7A	chr5:114504766-114506708	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr5:114504761-114506919	NB4	blood:	n/a	n/a
23	MXI1	chr5:114506226-114506629	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr5:114504747-114506529	Hela-S3	cervix:	n/a	n/a
25	MAX	chr5:114504939-114506633	A549	lung:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
26	MAX	chr5:114504652-114506973	NB4	blood:	n/a	chr5:114505836-114505846 chr5:114505785-114505792 chr5:114506464-114506474
27	E2F6	chr5:114504891-114506538	A549	lung:	n/a	chr5:114505148-114505160 chr5:114505940-114505950 chr5:114506232-114506242 chr5:114506184-114506193
28	REST	chr5:114504305-114506477	H1-neurons	neurons:	n/a	chr5:114505648-114505661 chr5:114506144-114506164 chr5:114505913-114505923 chr5:114506194-114506207 chr5:114506001-114506014 chr5:114506374-114506392
29	MXI1	chr5:114504459-114507462	SK-N-SH	brain:	n/a	chr5:114505673-114505688 chr5:114505675-114505690
30	E2F6	chr5:114505120-114506551	H1-hESC	embryonic stem cell:	n/a	chr5:114505148-114505160 chr5:114505940-114505950 chr5:114506232-114506242 chr5:114506184-114506193
31	POLR2A	chr5:114504847-114507120	SK-N-MC	brain:	n/a	n/a
32	BACH1	chr5:114506375-114506464	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:114506448-114506498	HPAEpiC	pulmonary alveolar:	n/a
2	chr5:114506448-114506498	HL-60	blood:	n/a
3	chr5:114506448-114506498	AG04450	lung:	fetal
4	chr5:114506448-114506498	HEEpiC	esophagus:	n/a
5	chr5:114506448-114506498	Jurkat	blood:	n/a
6	chr5:114506448-114506498	PrEC	prostate:	n/a
7	chr5:114506448-114506498	HUVEC	blood vessel:	n/a
8	chr5:114506448-114506498	GM12891	blood:	n/a
9	chr5:114506448-114506498	HEK293	kidney:	embryo
10	chr5:114506448-114506498	PANC-1	pancreas:	n/a
11	chr5:114506448-114506498	SKMC	muscle:	n/a
12	chr5:114506448-114506498	Caco-2	colon:	n/a
13	chr5:114506448-114506498	GM12878	blood:	n/a
14	chr5:114506448-114506498	GM12892	blood:	n/a
15	chr5:114506448-114506498	Hela-S3	cervix:	n/a
16	chr5:114506448-114506498	A549	lung:	n/a
17	chr5:114506448-114506498	HRPEpiC	eye:	n/a
18	chr5:114506448-114506498	MCF10A-Er-Src	breast:	n/a
19	chr5:114506448-114506498	HepG2	liver:	n/a
20	chr5:114506448-114506498	IMR90	lung:	fetal
21	chr5:114506448-114506498	SK-N-MC	brain:	n/a
22	chr5:114506448-114506498	SAEC	small airway:	n/a
23	chr5:114506448-114506498	AG10803	skin:	n/a
24	chr5:114506448-114506498	ECC-1	luminal epithelium:	n/a
25	chr5:114506448-114506498	LNCaP	prostate:	n/a
26	chr5:114506448-114506498	HCM	heart:	n/a
27	chr5:114506448-114506498	SK-N-SH_RA	brain:	n/a
28	chr5:114506448-114506498	RPTEC	kidney:	n/a
29	chr5:114506448-114506498	NT2-D1	testis:	n/a
30	chr5:114506448-114506498	BE2_C	brain:	n/a
31	chr5:114506448-114506498	AG09319	gingival:	n/a
32	chr5:114506448-114506498	HCPEpiC	choroid plexus:	n/a
33	chr5:114506448-114506498	Hepatocyte	liver:	n/a
34	chr5:114506448-114506498	U87	brain:	n/a
35	chr5:114506448-114506498	NH-A	brain:	n/a
36	chr5:114506448-114506498	HCT-116	colon:	n/a
37	chr5:114506448-114506498	GM19239	blood:	n/a
38	chr5:114506448-114506498	BJ	skin:	n/a
39	chr5:114506448-114506498	HMEC	breast:	n/a
40	chr5:114506448-114506498	GM06990	blood:	n/a
41	chr5:114506448-114506498	ProgFib	skin:	n/a
42	chr5:114506448-114506498	NHDF-neo	bronchial:	n/a
43	chr5:114506448-114506498	NB4	blood:	n/a
44	chr5:114506448-114506498	K562	blood:	n/a
45	chr5:114506448-114506498	MCF-7	breast:	n/a
46	chr5:114506448-114506498	HCF	heart:	n/a
47	chr5:114506448-114506498	HNPCEpiC	eye:	n/a
48	chr5:114506448-114506498	HAEpiC	amniotic membrane:	n/a
49	chr5:114506448-114506498	PFSK-1	brain:	n/a
50	chr5:114506448-114506498	HRCEpiC	kidney:	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:114504828..114507303-chr5:114508620..114510973,3	MCF-7	breast:
2	chr5:114504108..114507715-chr5:114515140..114518807,4	MCF-7	breast:
3	chr5:114504319..114509129-chr5:114509356..114517256,16	MCF-7	breast:
4	chr5:114505970..114507896-chr5:114509375..114511421,2	K562	blood:
5	chr5:114432281..114434501-chr5:114505854..114507519,2	MCF-7	breast:
6	chr5:114505745..114508021-chr5:114511446..114514175,2	K562	blood:

Variant related genes	Relation type
TRIM36	TF binding region
TRIM36	CpG island
ENSG00000152503	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10040143	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11745636	0.82[TSI][hapmap]
rs1610072	0.80[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1806346	0.82[EUR][1000 genomes]
rs2241974	0.84[CEU][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap]
rs3792863	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3805589	0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs3805590	0.85[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6594881	0.80[AMR][1000 genomes]
rs6859943	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6894360	0.80[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.92[TSI][hapmap]
rs7716390	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7719404	0.90[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7737426	0.84[CEU][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs973	0.85[AMR][1000 genomes];0.82[EUR][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	nsv830453	chr5:114277261-114546536	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv462399	chr5:114445023-114526010	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv599477	chr5:114445023-114526010	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv830454	chr5:114453864-114607159	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv3336600	chr5:114504203-114506901	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs973589	PGGT1B	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:114504200-114506600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:114504200-114506600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr5:114504200-114506600	Active TSS	Brain Angular Gyrus	brain
4	chr5:114504200-114506600	Active TSS	HSMMtube	muscle
5	chr5:114504200-114506800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:114504200-114507000	Active TSS	Brain Inferior Temporal Lobe	brain
7	chr5:114504200-114507400	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr5:114504400-114506600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:114504400-114506600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:114504600-114506600	Active TSS	H1 Cell Line	embryonic stem cell
11	chr5:114504600-114506600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr5:114504600-114506600	Active TSS	Aorta	Aorta
13	chr5:114504600-114506600	Active TSS	HSMM	muscle
14	chr5:114504600-114506800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:114504600-114506800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:114504600-114506800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:114504600-114506800	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr5:114504600-114507000	Active TSS	Rectal Smooth Muscle	rectum
19	chr5:114504600-114507600	Active TSS	Duodenum Mucosa	Duodenum
20	chr5:114504800-114506600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
21	chr5:114504800-114506600	Active TSS	Gastric	stomach
22	chr5:114504800-114506800	Active TSS	Pancreas	Pancrea
23	chr5:114504800-114507000	Bivalent/Poised TSS	Small Intestine	intestine
24	chr5:114504800-114507200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:114505000-114506600	Bivalent/Poised TSS	Fetal Kidney	kidney
26	chr5:114505000-114506800	Active TSS	Sigmoid Colon	Sigmoid Colon
27	chr5:114505200-114506600	Transcr. at gene 5' and 3'	Right Atrium	heart
28	chr5:114505200-114507000	Active TSS	Brain Substantia Nigra	brain
29	chr5:114505400-114506600	Active TSS	Ovary	ovary
30	chr5:114505400-114507200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:114505400-114507200	Active TSS	Colonic Mucosa	Colon
32	chr5:114505600-114506600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
33	chr5:114505800-114506600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:114506000-114506600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:114506000-114506600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
36	chr5:114506000-114506600	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr5:114506000-114506600	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
38	chr5:114506000-114506600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:114506000-114506600	Flanking Active TSS	Liver	Liver
40	chr5:114506000-114506600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
41	chr5:114506000-114506600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
42	chr5:114506000-114506600	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
43	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
44	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
47	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
48	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr5:114506000-114506800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin

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