Variant report

Variant	rs3749863
Chromosome Location	chr6:45345248-45345249
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	MYC	chr6:45345231-45346299	MCF-7	breast:	n/a	chr6:45345903-45345912
2	HMGN3	chr6:45344856-45346318	K562	blood:	n/a	n/a
3	ELF1	chr6:45345075-45346174	HCT-116	colon:	n/a	chr6:45345907-45345916
4	RCOR1	chr6:45344689-45346414	K562	blood:	n/a	n/a
5	POLR2A	chr6:45345012-45346295	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr6:45345050-45346115	HCT-116	colon:	n/a	n/a
7	MAX	chr6:45344752-45346455	A549	lung:	n/a	chr6:45345903-45345912
8	TAF1	chr6:45345002-45346367	K562	blood:	n/a	n/a
9	RAD21	chr6:45344768-45346441	Hela-S3	cervix:	n/a	chr6:45345480-45345492 chr6:45345207-45345220 chr6:45345692-45345701
10	POLR2A	chr6:45344999-45346412	H1-hESC	embryonic stem cell:	n/a	n/a
11	HDAC2	chr6:45345022-45346218	HepG2	liver:	n/a	chr6:45345784-45345793
12	PML	chr6:45344765-45346272	K562	blood:	n/a	n/a
13	TAF1	chr6:45344940-45346364	Hela-S3	cervix:	n/a	n/a
14	TEAD4	chr6:45344201-45346488	K562	blood:	n/a	n/a
15	CTCF	chr6:45345118-45346114	GM12878	blood:	n/a	n/a
16	TBL1XR1	chr6:45344788-45346914	K562	blood:	n/a	n/a
17	REST	chr6:45345136-45346309	K562	blood:	n/a	chr6:45345310-45345323 chr6:45345479-45345492 chr6:45345301-45345314 chr6:45345289-45345299
18	E2F6	chr6:45345122-45345653	K562	blood:	n/a	chr6:45345240-45345248 chr6:45345397-45345406 chr6:45345241-45345248 chr6:45345240-45345248
19	GTF2F1	chr6:45344736-45346137	K562	blood:	n/a	n/a
20	YY1	chr6:45345179-45346178	A549	lung:	n/a	chr6:45345849-45345863 chr6:45345693-45345701 chr6:45345212-45345223 chr6:45345907-45345916 chr6:45345397-45345411 chr6:45345852-45345861
21	MAFK	chr6:45344718-45346223	Hela-S3	cervix:	n/a	n/a
22	GABPA	chr6:45345177-45346367	MCF-7	breast:	n/a	chr6:45345779-45345793 chr6:45345782-45345796 chr6:45345782-45345791 chr6:45345784-45345793 chr6:45345852-45345861 chr6:45345782-45345793
23	CTCF	chr6:45345200-45345350	NHDF-neo	bronchial:	n/a	n/a
24	GTF2B	chr6:45344848-45346303	K562	blood:	n/a	n/a
25	ELF1	chr6:45345077-45345998	K562	blood:	n/a	chr6:45345907-45345916
26	POU2F2	chr6:45344938-45346216	GM12878	blood:	n/a	chr6:45345717-45345729
27	POLR2A	chr6:45344694-45346441	Raji	blood:	n/a	n/a
28	PML	chr6:45345184-45346194	MCF-7	breast:	n/a	n/a
29	TEAD4	chr6:45345060-45346220	ECC-1	luminal epithelium:	n/a	n/a
30	ZNF384	chr6:45345049-45346550	K562	blood:	n/a	n/a
31	POLR2A	chr6:45344357-45346382	PBDE	blood:	n/a	n/a
32	ZNF143	chr6:45345026-45346128	GM12878	blood:	n/a	chr6:45345296-45345306 chr6:45345923-45345942 chr6:45345397-45345407
33	YY1	chr6:45345087-45346330	ECC-1	luminal epithelium:	n/a	chr6:45345849-45345863 chr6:45345693-45345701 chr6:45345212-45345223 chr6:45345907-45345916 chr6:45345397-45345411 chr6:45345852-45345861
34	YY1	chr6:45344847-45346436	SK-N-SH_RA	brain:	n/a	chr6:45345849-45345863 chr6:45346359-45346368 chr6:45345693-45345701 chr6:45345212-45345223 chr6:45345907-45345916 chr6:45345397-45345411 chr6:45345852-45345861
35	CHD1	chr6:45345122-45345250	GM12878	blood:	n/a	n/a
36	MAX	chr6:45344579-45346312	HCT-116	colon:	n/a	chr6:45345903-45345912
37	POLR2A	chr6:45345091-45346327	GM19193	blood:	n/a	n/a
38	CTCF	chr6:45345207-45345378	MCF-7	breast:	n/a	n/a
39	TAF1	chr6:45345155-45346204	A549	lung:	n/a	n/a
40	RFX5	chr6:45344954-45346388	Hela-S3	cervix:	n/a	n/a
41	ELK1	chr6:45345199-45346455	GM12878	blood:	n/a	n/a
42	POLR2A	chr6:45344646-45346758	Hela-S3	cervix:	n/a	n/a
43	E2F6	chr6:45345103-45346208	A549	lung:	n/a	chr6:45345852-45345861 chr6:45345783-45345792 chr6:45345240-45345248 chr6:45345397-45345406 chr6:45345241-45345248 chr6:45345240-45345248
44	POLR2A	chr6:45344906-45346343	GM18951	blood:	n/a	n/a
45	RAD21	chr6:45345123-45345497	HepG2	liver:	n/a	chr6:45345480-45345492 chr6:45345207-45345220
46	ZNF263	chr6:45344741-45346371	HEK293-T-REx	kidney:	n/a	chr6:45345249-45345258
47	ZBTB7A	chr6:45344943-45345966	ECC-1	luminal epithelium:	n/a	chr6:45345801-45345810
48	YY1	chr6:45345067-45346041	GM12891	blood:	n/a	chr6:45345849-45345863 chr6:45345693-45345701 chr6:45345212-45345223 chr6:45345907-45345916 chr6:45345397-45345411 chr6:45345852-45345861
49	EGR1	chr6:45345127-45345976	GM12878	blood:	n/a	chr6:45345165-45345175 chr6:45345783-45345792 chr6:45345554-45345568 chr6:45345231-45345246 chr6:45345852-45345862 chr6:45345720-45345733
50	TEAD4	chr6:45345208-45346113	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:74033540..74034519-chr6:45344800..45345751,2	Hela-S3	cervix:
2	chr6:45343131..45346998-chr6:45386286..45389886,4	MCF-7	breast:
3	chr6:45290102..45292496-chr6:45343857..45345735,2	K562	blood:
4	chr6:45332930..45339216-chr6:45342239..45349440,11	K562	blood:
5	chr12:56511321..56512580-chr6:45345090..45346296,3	Hela-S3	cervix:
6	chr6:45293709..45297564-chr6:45344489..45347736,3	K562	blood:
7	chr6:45345113..45345957-chr7:138793766..138794794,3	Hela-S3	cervix:
8	chr6:45328959..45331419-chr6:45344647..45347032,2	MCF-7	breast:
9	chr6:45331868..45334575-chr6:45344958..45347495,2	MCF-7	breast:

Variant related genes	Relation type
SUPT3H	TF binding region
ENSG00000105939	Chromatin interaction
ENSG00000271857	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000196284	Chromatin interaction
ENSG00000168209	Chromatin interaction
ENSG00000124813	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10948222	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs12199720	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs12205312	0.92[EUR][1000 genomes]
rs12207402	1.00[YRI][hapmap]
rs1321081	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs17209755	1.00[YRI][hapmap]
rs2396425	0.89[CEU][hapmap]
rs2396502	0.95[EUR][1000 genomes]
rs3923353	0.88[EUR][1000 genomes]
rs4373351	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4446571	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs4506035	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4510673	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs4631280	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6458441	0.96[EUR][1000 genomes]
rs6934594	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs6935398	0.88[EUR][1000 genomes]
rs7451423	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs7740083	0.92[EUR][1000 genomes]
rs7770401	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9296453	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs9296457	0.84[EUR][1000 genomes]
rs9357480	0.88[CEU][hapmap]
rs9357484	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs9369552	0.80[EUR][1000 genomes]
rs9369558	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs9381383	0.91[EUR][1000 genomes]
rs9395084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs9395086	0.82[EUR][1000 genomes]
rs9395087	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9395095	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs9463078	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9463081	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs9463083	0.90[EUR][1000 genomes]
rs9472460	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3749863	SUPT3H	cis	multi-tissue	Pritchard
rs3749863	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45343800-45346800	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:45344000-45346800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:45344000-45346800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:45344000-45347000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:45344200-45346400	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:45344200-45346400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:45344200-45346400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:45344200-45346400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:45344200-45346600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:45344200-45346600	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:45344200-45346800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:45344200-45347000	Active TSS	NHLF	lung
13	chr6:45344400-45346400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:45344400-45346600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr6:45344400-45346600	Active TSS	Right Ventricle	heart
16	chr6:45344400-45346800	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr6:45344400-45346800	Active TSS	A549	lung
18	chr6:45344400-45347200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:45344600-45346000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:45344600-45346200	Active TSS	Muscle Satellite Cultured Cells	--
21	chr6:45344600-45346200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:45344600-45346200	Active TSS	Colonic Mucosa	Colon
23	chr6:45344600-45346400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:45344600-45346400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:45344600-45346400	Active TSS	Aorta	Aorta
26	chr6:45344600-45346400	Active TSS	Fetal Intestine Large	intestine
27	chr6:45344600-45346400	Active TSS	Fetal Kidney	kidney
28	chr6:45344600-45346600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:45344600-45346600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:45344600-45346600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:45344600-45346600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:45344600-45346600	Active TSS	Colon Smooth Muscle	Colon
33	chr6:45344600-45346600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:45344600-45346600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr6:45344600-45346600	Active TSS	Fetal Heart	heart
36	chr6:45344600-45346600	Active TSS	Fetal Muscle Trunk	muscle
37	chr6:45344600-45346600	Active TSS	Fetal Stomach	stomach
38	chr6:45344600-45346600	Active TSS	Psoas Muscle	Psoas
39	chr6:45344600-45346600	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr6:45344600-45346600	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr6:45344600-45346600	Active TSS	Stomach Smooth Muscle	stomach
42	chr6:45344600-45346600	Active TSS	Monocytes-CD14+_RO01746	blood
43	chr6:45344600-45346800	Active TSS	Brain Cingulate Gyrus	brain
44	chr6:45344600-45346800	Active TSS	Fetal Muscle Leg	muscle
45	chr6:45344600-45347000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr6:45344600-45347200	Active TSS	K562	blood
47	chr6:45344800-45346200	Bivalent/Poised TSS	HepG2	liver
48	chr6:45344800-45346400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:45344800-45346400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:45344800-45346400	Active TSS	HUES64 Cell Line	embryonic stem cell

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