Variant report

Variant	rs6781327
Chromosome Location	chr3:42774604-42774605
allele	C/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	FOXA1	chr3:42773652-42774836	HepG2	liver:	n/a	n/a
2	CTCF	chr3:42774460-42774610	K562	blood:	n/a	chr3:42774551-42774560
3	MAX	chr3:42773717-42774693	HepG2	liver:	n/a	n/a
4	CTCF	chr3:42774480-42774630	Caco-2	colon:	n/a	chr3:42774551-42774560
5	RAD21	chr3:42774360-42774717	HepG2	liver:	n/a	chr3:42774542-42774555
6	ELF1	chr3:42774275-42774659	HepG2	liver:	n/a	n/a
7	CTCF	chr3:42774460-42774610	HCPEpiC	choroid plexus:	n/a	chr3:42774551-42774560
8	CTCF	chr3:42774460-42774610	GM12870	blood:	n/a	chr3:42774551-42774560
9	HSF1	chr3:42773735-42774883	HepG2	liver:	n/a	chr3:42774093-42774108
10	CTCF	chr3:42774460-42774610	NHDF-neo	bronchial:	n/a	chr3:42774551-42774560
11	CTCF	chr3:42774500-42774650	WERI-Rb-1	eye:	n/a	chr3:42774551-42774560
12	NFIC	chr3:42773665-42774687	HepG2	liver:	n/a	n/a
13	HEY1	chr3:42773587-42774701	HepG2	liver:	n/a	n/a
14	CTCF	chr3:42774500-42774650	SK-N-SH_RA	brain:	n/a	chr3:42774551-42774560
15	MBD4	chr3:42773865-42774791	HepG2	liver:	n/a	n/a
16	CTCF	chr3:42774460-42774610	GM12865	blood:	n/a	chr3:42774551-42774560
17	CTCF	chr3:42774460-42774610	HepG2	liver:	n/a	chr3:42774551-42774560
18	CTCF	chr3:42774560-42774710	AG09309	skin:	n/a	n/a
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	chr3:42774480-42774630	HAc	cerebellar:	n/a	chr3:42774551-42774560
22	CTCF	chr3:42774480-42774630	GM12873	blood:	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	CTCF	chr3:42774500-42774650	HepG2	liver:	n/a	chr3:42774551-42774560
29	NFIC	chr3:42773652-42774795	HepG2	liver:	n/a	n/a
30	CTCF	chr3:42774460-42774610	MCF-7	breast:	n/a	chr3:42774551-42774560
31	CTCF	chr3:42774460-42774610	BJ	skin:	n/a	chr3:42774551-42774560
32	CTCF	chr3:42774540-42774690	HCT-116	colon:	n/a	chr3:42774551-42774560
33	CTCF	chr3:42774500-42774650	HBMEC	blood vessel:	n/a	chr3:42774551-42774560
34	CTCF	chr3:42774520-42774670	HFF-Myc	foreskin:	n/a	chr3:42774551-42774560
35	FOXA2	chr3:42774436-42774750	HepG2	liver:	n/a	n/a
36	CTCF	chr3:42774470-42774615	Hela-S3	cervix:	n/a	chr3:42774551-42774560
37	CTCF	chr3:42774460-42774610	HEK293	kidney:	n/a	chr3:42774551-42774560
38	POLR2A	chr3:42773525-42774674	HepG2	liver:	n/a	n/a
39	CTCF	chr3:42774372-42774669	HepG2	liver:	n/a	chr3:42774551-42774560
40	CTCF	chr3:42774520-42774670	HEEpiC	esophagus:	n/a	chr3:42774551-42774560
41	CTCF	chr3:42774520-42774670	NB4	blood:	n/a	chr3:42774551-42774560
42	CTCF	chr3:42774480-42774630	WERI-Rb-1	eye:	n/a	chr3:42774551-42774560
43	CTCF	chr3:42774401-42774697	K562	blood:	n/a	chr3:42774551-42774560
44	MYBL2	chr3:42773515-42774763	HepG2	liver:	n/a	n/a
45	MXI1	chr3:42773631-42774714	HepG2	liver:	n/a	n/a
46	RCOR1	chr3:42773677-42774726	HepG2	liver:	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	chr3:42774480-42774630	HCM	heart:	n/a	chr3:42774551-42774560
50	CTCF	chr3:42774446-42774654	MCF-7	breast:	n/a	chr3:42774551-42774560

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42700054..42702957-chr3:42774515..42776215,2	K562	blood:

Variant related genes	Relation type
CCDC13	TF binding region
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs6768001	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6773675	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6777653	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6783035	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6792887	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6794170	0.83[AFR][1000 genomes]
rs6802779	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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

No data

Chromatin state (count:43 , 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	chr3:42773000-42778400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:42773200-42776800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:42773600-42775200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:42773600-42775600	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr3:42773600-42776400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:42773800-42775400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:42773800-42775400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:42773800-42775600	Enhancers	Brain Germinal Matrix	brain
19	chr3:42773800-42776600	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:42773800-42776800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:42773800-42777600	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:42774000-42774800	Flanking Active TSS	HepG2	liver
23	chr3:42774000-42775200	Flanking Active TSS	Brain Substantia Nigra	brain
24	chr3:42774000-42775400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:42774000-42776400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:42774000-42776400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr3:42774000-42777400	Weak transcription	Right Ventricle	heart
28	chr3:42774200-42775600	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr3:42774200-42775600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:42774200-42777800	Weak transcription	Right Atrium	heart
31	chr3:42774200-42778200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr3:42774200-42778200	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr3:42774400-42774800	Enhancers	Fetal Heart	heart
34	chr3:42774400-42775400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:42774400-42775600	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr3:42774400-42776000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr3:42774400-42776000	Enhancers	H9 Cell Line	embryonic stem cell
38	chr3:42774600-42774800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
39	chr3:42774600-42775000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr3:42774600-42775000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr3:42774600-42775000	Active TSS	Brain Anterior Caudate	brain
42	chr3:42774600-42775200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:42774600-42780800	Weak transcription	Psoas Muscle	Psoas

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