Variant report

Variant	rs17074778
Chromosome Location	chr3:42774475-42774476
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	FOXA1	chr3:42773652-42774836	HepG2	liver:	n/a	n/a
2	CTCF	chr3:42774460-42774610	K562	blood:	n/a	chr3:42774551-42774560
3	CTCF	chr3:42774420-42774570	HFF-Myc	foreskin:	n/a	chr3:42774551-42774560
4	CTCF	chr3:42774440-42774590	GM12868	blood:	n/a	chr3:42774551-42774560
5	CTCF	chr3:42774440-42774590	BJ	skin:	n/a	chr3:42774551-42774560
6	MAX	chr3:42773717-42774693	HepG2	liver:	n/a	n/a
7	RAD21	chr3:42774360-42774717	HepG2	liver:	n/a	chr3:42774542-42774555
8	ELF1	chr3:42774275-42774659	HepG2	liver:	n/a	n/a
9	CTCF	chr3:42774460-42774610	HCPEpiC	choroid plexus:	n/a	chr3:42774551-42774560
10	CTCF	chr3:42774460-42774610	GM12870	blood:	n/a	chr3:42774551-42774560
11	HSF1	chr3:42773735-42774883	HepG2	liver:	n/a	chr3:42774093-42774108
12	CTCF	chr3:42774460-42774610	NHDF-neo	bronchial:	n/a	chr3:42774551-42774560
13	ARID3A	chr3:42774377-42774577	HepG2	liver:	n/a	n/a
14	NFIC	chr3:42773665-42774687	HepG2	liver:	n/a	n/a
15	HEY1	chr3:42773587-42774701	HepG2	liver:	n/a	n/a
16	MBD4	chr3:42773865-42774791	HepG2	liver:	n/a	n/a
17	CTCF	chr3:42774460-42774610	GM12865	blood:	n/a	chr3:42774551-42774560
18	CTCF	chr3:42774460-42774610	HepG2	liver:	n/a	chr3:42774551-42774560
19	RAD21	chr3:42773774-42774752	HepG2	liver:	n/a	chr3:42774542-42774555
20	MYBL2	chr3:42773551-42774741	HepG2	liver:	n/a	n/a
21	CTCF	chr3:42774440-42774590	AG04450	lung:	n/a	chr3:42774551-42774560
22	CTCF	chr3:42774440-42774590	HMEC	breast:	n/a	chr3:42774551-42774560
23	CTCF	chr3:42774428-42774635	MCF-7	breast:	n/a	chr3:42774551-42774560
24	CHD2	chr3:42774368-42774673	HepG2	liver:	n/a	n/a
25	CTCF	chr3:42774446-42774631	MCF-7	breast:	n/a	chr3:42774551-42774560
26	CTBP2	chr3:42774370-42775579	H1-hESC	embryonic stem cell:	n/a	n/a
27	CTCF	chr3:42774392-42774707	K562	blood:	n/a	chr3:42774551-42774560
28	NFIC	chr3:42773652-42774795	HepG2	liver:	n/a	n/a
29	CTCF	chr3:42774460-42774610	MCF-7	breast:	n/a	chr3:42774551-42774560
30	CTCF	chr3:42774460-42774610	BJ	skin:	n/a	chr3:42774551-42774560
31	CTCF	chr3:42774420-42774570	GM12872	blood:	n/a	chr3:42774551-42774560
32	MYC	chr3:42774438-42774579	HepG2	liver:	n/a	n/a
33	FOXA2	chr3:42774436-42774750	HepG2	liver:	n/a	n/a
34	CTCF	chr3:42774470-42774615	Hela-S3	cervix:	n/a	chr3:42774551-42774560
35	CTCF	chr3:42774380-42774530	RPTEC	kidney:	n/a	n/a
36	CTCF	chr3:42774460-42774610	HEK293	kidney:	n/a	chr3:42774551-42774560
37	CTCF	chr3:42774380-42774530	AG04450	lung:	n/a	n/a
38	POLR2A	chr3:42773525-42774674	HepG2	liver:	n/a	n/a
39	CTCF	chr3:42774420-42774570	AoAF	blood vessel:	n/a	chr3:42774551-42774560
40	CTCF	chr3:42774372-42774669	HepG2	liver:	n/a	chr3:42774551-42774560
41	CTCF	chr3:42774401-42774697	K562	blood:	n/a	chr3:42774551-42774560
42	MYBL2	chr3:42773515-42774763	HepG2	liver:	n/a	n/a
43	MXI1	chr3:42773631-42774714	HepG2	liver:	n/a	n/a
44	POLR2A	chr3:42773734-42774534	HepG2	liver:	n/a	n/a
45	RCOR1	chr3:42773677-42774726	HepG2	liver:	n/a	n/a
46	CTCF	chr3:42774400-42774550	GM12864	blood:	n/a	n/a
47	ELF1	chr3:42774310-42774669	HepG2	liver:	n/a	n/a
48	EP300	chr3:42773672-42774721	HepG2	liver:	n/a	n/a
49	CTCF	chr3:42774446-42774654	MCF-7	breast:	n/a	chr3:42774551-42774560
50	CTCF	chr3:42774420-42774570	SAEC	small airway:	n/a	chr3:42774551-42774560

Variant related genes	Relation type
CCDC13	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10461012	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10865921	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865923	0.89[EUR][1000 genomes]
rs11129969	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs11129970	0.98[EUR][1000 genomes]
rs11709054	0.95[EUR][1000 genomes]
rs11709500	0.94[CEU][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes]
rs11713172	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs11915803	0.84[CEU][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs17238314	0.98[EUR][1000 genomes]
rs17238798	0.81[GIH][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs2240861	0.94[CEU][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes]
rs34110933	0.95[EUR][1000 genomes]
rs4682856	0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs55884426	0.97[EUR][1000 genomes]
rs55904344	0.96[EUR][1000 genomes]
rs59478814	0.97[EUR][1000 genomes]
rs59713146	0.98[EUR][1000 genomes]
rs60049195	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60176972	0.88[EUR][1000 genomes]
rs62246603	0.96[EUR][1000 genomes]
rs62246606	0.95[EUR][1000 genomes]
rs62246635	0.85[EUR][1000 genomes]
rs62250113	0.95[EUR][1000 genomes]
rs62250114	0.96[EUR][1000 genomes]
rs6442057	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs9836162	0.94[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.95[EUR][1000 genomes]
rs9837412	0.88[EUR][1000 genomes]
rs9838388	0.89[CEU][hapmap];0.87[EUR][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	nsv1013578	chr3:42747858-42817321	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv999713	chr3:42749022-42817321	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17074778	FYCO1	cis	cerebellum	SCAN
rs17074778	HHATL	cis	cerebellum	SCAN
rs17074778	LRRC2	cis	cerebellum	SCAN
rs17074778	HHATL	cis	parietal	SCAN
rs17074778	ZNF35	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42763600-42774800	Enhancers	Brain Angular Gyrus	brain
2	chr3:42768600-42776000	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:42769000-42774800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:42769000-42775000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr3:42769600-42785600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:42769800-42787600	Weak transcription	Gastric	stomach
7	chr3:42770600-42775600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr3:42771200-42775800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr3:42772600-42777600	Weak transcription	Left Ventricle	heart
10	chr3:42772600-42778200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr3:42773000-42774600	Enhancers	Pancreas	Pancrea
12	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:42773400-42774600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:42773600-42774600	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr3:42773600-42775200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:42773600-42775600	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr3:42773600-42776400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:42773800-42774600	Enhancers	Psoas Muscle	Psoas
20	chr3:42773800-42775400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:42773800-42775400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:42773800-42775600	Enhancers	Brain Germinal Matrix	brain
23	chr3:42773800-42776600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr3:42773800-42776800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:42773800-42777600	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:42774000-42774800	Flanking Active TSS	HepG2	liver
27	chr3:42774000-42775200	Flanking Active TSS	Brain Substantia Nigra	brain
28	chr3:42774000-42775400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:42774000-42776400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:42774000-42776400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr3:42774000-42777400	Weak transcription	Right Ventricle	heart
32	chr3:42774200-42774600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr3:42774200-42774600	Enhancers	Fetal Muscle Trunk	muscle
34	chr3:42774200-42775600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:42774200-42775600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:42774200-42777800	Weak transcription	Right Atrium	heart
37	chr3:42774200-42778200	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr3:42774200-42778200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:42774400-42774600	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr3:42774400-42774800	Enhancers	Fetal Heart	heart
41	chr3:42774400-42775400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:42774400-42775600	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr3:42774400-42776000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr3:42774400-42776000	Enhancers	H9 Cell Line	embryonic stem cell

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