Variant report

Variant	rs4945831
Chromosome Location	chr6:109761437-109761438
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	PAX5	chr6:109761366-109762468	GM12892	blood:	n/a	n/a
2	SETDB1	chr6:109761307-109762511	K562	blood:	n/a	n/a
3	NR2F2	chr6:109760986-109762085	K562	blood:	n/a	n/a
4	NR2F2	chr6:109761276-109762393	MCF-7	breast:	n/a	n/a
5	E2F6	chr6:109761329-109761874	A549	lung:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572
6	POLR2A	chr6:109761401-109763076	H1-neurons	neurons:	n/a	n/a
7	ZBTB7A	chr6:109761340-109761887	ECC-1	luminal epithelium:	n/a	chr6:109761473-109761487
8	MAX	chr6:109761403-109762247	HUVEC	blood vessel:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
9	E2F6	chr6:109761274-109762704	K562	blood:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572 chr6:109762207-109762216 chr6:109762209-109762219
10	E2F6	chr6:109761330-109762952	H1-hESC	embryonic stem cell:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572 chr6:109762207-109762216 chr6:109762209-109762219
11	POLR2A	chr6:109761435-109763358	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr6:109761405-109762298	ECC-1	luminal epithelium:	n/a	chr6:109761903-109761919 chr6:109761880-109761896 chr6:109761866-109761882
13	MXI1	chr6:109760621-109763112	SK-N-SH	brain:	n/a	chr6:109762145-109762160 chr6:109761832-109761847
14	ZBTB7A	chr6:109761331-109762684	K562	blood:	n/a	chr6:109761473-109761487
15	RCOR1	chr6:109761048-109762700	GM12878	blood:	n/a	n/a
16	MYC	chr6:109761346-109762787	K562	blood:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
17	YY1	chr6:109761414-109762364	HepG2	liver:	n/a	chr6:109761872-109761886 chr6:109762202-109762216 chr6:109761858-109761867 chr6:109761618-109761632 chr6:109761563-109761572 chr6:109761527-109761538
18	TAL1	chr6:109761392-109762036	K562	blood:	n/a	n/a
19	TBP	chr6:109760869-109762954	K562	blood:	n/a	n/a
20	MAX	chr6:109761365-109762285	SK-N-SH	brain:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
21	ZBTB7A	chr6:109761312-109762124	K562	blood:	n/a	chr6:109761473-109761487
22	YY1	chr6:109761381-109762257	GM12878	blood:	n/a	chr6:109761872-109761886 chr6:109762202-109762216 chr6:109761858-109761867 chr6:109761618-109761632 chr6:109761563-109761572 chr6:109761527-109761538
23	MAX	chr6:109761366-109762869	GM12878	blood:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
24	TCF12	chr6:109761274-109762326	A549	lung:	n/a	n/a
25	HCFC1	chr6:109761064-109762978	Hela-S3	cervix:	n/a	n/a
26	MXI1	chr6:109760770-109762521	Hela-S3	cervix:	n/a	chr6:109762145-109762160 chr6:109761832-109761847
27	MAX	chr6:109761323-109762879	H1-hESC	embryonic stem cell:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
28	MYC	chr6:109761346-109762872	K562	blood:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
29	E2F6	chr6:109761218-109762764	A549	lung:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572 chr6:109762207-109762216 chr6:109762209-109762219
30	UBTF	chr6:109760909-109762895	K562	blood:	n/a	n/a
31	MAX	chr6:109761267-109763135	HCT-116	colon:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
32	EGR1	chr6:109761333-109762895	HCT-116	colon:	n/a	chr6:109761875-109761885 chr6:109761894-109761907 chr6:109761454-109761467 chr6:109761562-109761572 chr6:109761854-109761864 chr6:109761454-109761467 chr6:109761856-109761869
33	MAX	chr6:109761359-109762783	MCF-7	breast:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
34	HA-E2F1	chr6:109761357-109762532	MCF-7	breast:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572 chr6:109762207-109762216 chr6:109762209-109762219
35	YY1	chr6:109761422-109762165	SK-N-SH_RA	brain:	n/a	chr6:109761872-109761886 chr6:109761858-109761867 chr6:109761618-109761632 chr6:109761563-109761572 chr6:109761527-109761538
36	REST	chr6:109761176-109762431	H1-neurons	neurons:	n/a	n/a
37	MAZ	chr6:109761351-109762706	K562	blood:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
38	POLR2A	chr6:109761385-109762815	K562	blood:	n/a	n/a
39	SIN3AK20	chr6:109761363-109762915	MCF-7	breast:	n/a	n/a
40	POLR2A	chr6:109760888-109762727	IMR90	lung:	n/a	n/a
41	E2F6	chr6:109761340-109762120	K562	blood:	n/a	chr6:109761583-109761593 chr6:109761855-109761864 chr6:109761875-109761884 chr6:109761453-109761462 chr6:109761577-109761586 chr6:109761563-109761572
42	EP300	chr6:109761403-109762314	SK-N-SH	brain:	n/a	chr6:109761903-109761919 chr6:109761880-109761896 chr6:109761866-109761882
43	TAF1	chr6:109761434-109762476	ECC-1	luminal epithelium:	n/a	n/a
44	YY1	chr6:109761426-109762234	GM12892	blood:	n/a	chr6:109761872-109761886 chr6:109762202-109762216 chr6:109761858-109761867 chr6:109761618-109761632 chr6:109761563-109761572 chr6:109761527-109761538
45	POLR2A	chr6:109761408-109762977	HL-60	blood:	n/a	n/a
46	ELF1	chr6:109761360-109762285	K562	blood:	n/a	chr6:109761452-109761464 chr6:109761858-109761867 chr6:109761854-109761866 chr6:109761795-109761807 chr6:109762102-109762113
47	BHLHE40	chr6:109761432-109762376	GM12878	blood:	n/a	n/a
48	MAX	chr6:109761362-109762978	H1-hESC	embryonic stem cell:	n/a	chr6:109761564-109761574 chr6:109762181-109762190
49	PAX5	chr6:109761308-109761559	GM12878	blood:	n/a	n/a
50	MAX	chr6:109761296-109762906	K562	blood:	n/a	chr6:109761564-109761574 chr6:109762181-109762190

No.	Distal block	Cell Line	Cell type
1	chr6:109747606..109757389-chr6:109757828..109761794,11	K562	blood:
2	chr6:109415348..109417479-chr6:109760287..109762549,2	K562	blood:
3	chr6:109702383..109706611-chr6:109760202..109762116,4	K562	blood:
4	chr6:109759652..109764361-chr6:109800705..109806354,8	K562	blood:
5	chr6:109414651..109418067-chr6:109760738..109763991,4	MCF-7	breast:
6	chr6:109702022..109707287-chr6:109760251..109763953,8	MCF-7	breast:
7	chr6:109760182..109762059-chr6:109802883..109805670,2	MCF-7	breast:
8	chr6:109759628..109764398-chr6:109803414..109806709,4	K562	blood:
9	chr6:108880181..108882285-chr6:109761167..109763162,2	MCF-7	breast:
10	chr6:109702065..109705528-chr6:109760483..109765471,8	MCF-7	breast:
11	chr6:109760146..109763576-chr6:109804047..109805770,3	MCF-7	breast:
12	chr6:109752212..109757242-chr6:109759553..109764133,7	MCF-7	breast:

Variant related genes	Relation type
SMPD2	TF binding region
ENSG00000239160	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000112365	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000183137	Chromatin interaction
ENSG00000185250	Chromatin interaction
ENSG00000118689	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1046943	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1074765	0.94[EUR][1000 genomes]
rs1074766	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10872033	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11251	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12214147	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12529733	0.88[EUR][1000 genomes]
rs13219952	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1476387	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1521907	0.93[EUR][1000 genomes]
rs17070591	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1853330	0.85[EUR][1000 genomes]
rs1885690	0.93[EUR][1000 genomes]
rs1885691	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1998811	0.80[EUR][1000 genomes]
rs2211288	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2236084	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2277113	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884037	0.93[EUR][1000 genomes]
rs35146243	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35260632	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3734652	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3757230	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3757231	0.95[EUR][1000 genomes]
rs3757235	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3778474	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3778478	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3799842	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3818933	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4636056	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4946967	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4946970	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4946976	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58644322	0.93[EUR][1000 genomes]
rs59597139	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6914216	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6920372	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6939548	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6939953	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs699700	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs730089	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs736830	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs746794	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7748669	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7751582	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7754650	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7768973	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8465	0.94[EUR][1000 genomes]
rs910730	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9320286	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9372213	0.82[EUR][1000 genomes]
rs9398202	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9480947	0.95[EUR][1000 genomes]
rs9480949	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480956	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9480958	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487064	0.88[EUR][1000 genomes]
rs9487066	0.86[EUR][1000 genomes]
rs9487069	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487070	0.94[EUR][1000 genomes]
rs9487076	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9487084	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9487085	0.93[EUR][1000 genomes]
rs9487103	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs974034	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9791241	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3344959	chr6:109760484-109763032	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4945831	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs4945831	RP11-425D10.10	cis	Whole Blood	GTEx
rs4945831	MICAL1	cis	Artery Tibial	GTEx
rs4945831	SMPD2	cis	Whole Blood	GTEx
rs4945831	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs4945831	SMPD2	cis	Esophagus Mucosa	GTEx
rs4945831	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109760200-109761600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
2	chr6:109760200-109763200	Active TSS	A549	lung
3	chr6:109760400-109761600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:109760400-109762400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:109760400-109762400	Active TSS	Duodenum Mucosa	Duodenum
6	chr6:109760400-109762600	Active TSS	Ovary	ovary
7	chr6:109760400-109762600	Active TSS	Rectal Smooth Muscle	rectum
8	chr6:109760400-109762800	Active TSS	Fetal Intestine Small	intestine
9	chr6:109760400-109763400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:109760600-109761600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr6:109760600-109762400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:109760600-109762400	Active TSS	Colonic Mucosa	Colon
13	chr6:109760600-109762600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:109760600-109762600	Active TSS	Aorta	Aorta
15	chr6:109760600-109762600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr6:109760600-109762600	Active TSS	Fetal Intestine Large	intestine
17	chr6:109760600-109762800	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:109760800-109761600	Flanking Active TSS	HUVEC	blood vessel
19	chr6:109760800-109761800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:109760800-109762400	Active TSS	Brain Germinal Matrix	brain
21	chr6:109760800-109762600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:109760800-109762600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:109760800-109762600	Active TSS	Brain Angular Gyrus	brain
24	chr6:109760800-109762600	Active TSS	Brain Cingulate Gyrus	brain
25	chr6:109760800-109762600	Active TSS	Brain Hippocampus Middle	brain
26	chr6:109760800-109762600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr6:109760800-109762600	Active TSS	Esophagus	oesophagus
28	chr6:109760800-109762600	Active TSS	Pancreas	Pancrea
29	chr6:109760800-109762600	Active TSS	Right Atrium	heart
30	chr6:109760800-109762600	Active TSS	Stomach Mucosa	stomach
31	chr6:109760800-109762600	Active TSS	NHLF	lung
32	chr6:109760800-109762800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:109760800-109762800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr6:109760800-109762800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:109760800-109762800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:109760800-109762800	Active TSS	Colon Smooth Muscle	Colon
37	chr6:109760800-109762800	Active TSS	Gastric	stomach
38	chr6:109761000-109761600	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr6:109761000-109761600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr6:109761000-109761600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:109761000-109761600	Flanking Active TSS	Fetal Thymus	thymus
42	chr6:109761000-109761800	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr6:109761000-109761800	Flanking Active TSS	Dnd41	blood
44	chr6:109761000-109762400	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr6:109761000-109762400	Active TSS	Fetal Muscle Trunk	muscle
46	chr6:109761000-109762600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:109761000-109762600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr6:109761000-109762600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr6:109761000-109762600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:109761000-109762600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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