Variant report

Variant	rs732395
Chromosome Location	chr6:28616327-28616328
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:77)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:77 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZKSCAN1	chr6:28615883-28616804	Hela-S3	cervix:	n/a	n/a
2	ATF3	chr6:28615674-28616479	A549	lung:	n/a	n/a
3	TBP	chr6:28615853-28616373	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:28615816-28616795	SK-N-MC	brain:	n/a	n/a
5	GTF2F1	chr6:28615896-28616616	Hela-S3	cervix:	n/a	n/a
6	MYBL2	chr6:28615665-28616901	HepG2	liver:	n/a	chr6:28616636-28616646
7	TEAD4	chr6:28615834-28616546	K562	blood:	n/a	n/a
8	MAX	chr6:28615887-28616814	NB4	blood:	n/a	n/a
9	ATF3	chr6:28615700-28616420	HCT-116	colon:	n/a	n/a
10	NFIC	chr6:28615787-28616715	HepG2	liver:	n/a	n/a
11	SMC3	chr6:28615899-28616773	Hela-S3	cervix:	n/a	n/a
12	TEAD4	chr6:28615747-28616609	ECC-1	luminal epithelium:	n/a	n/a
13	MAFK	chr6:28615806-28616533	Hela-S3	cervix:	n/a	chr6:28616468-28616479
14	CEBPB	chr6:28615902-28616887	Hela-S3	cervix:	n/a	chr6:28616559-28616571
15	TEAD4	chr6:28615807-28616331	MCF-7	breast:	n/a	n/a
16	KAP1	chr6:28615780-28617033	HEK293	kidney:	n/a	chr6:28616591-28616599
17	BACH1	chr6:28615864-28616599	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF7L2	chr6:28615925-28616402	PANC-1	pancreas:	n/a	n/a
19	SIN3A	chr6:28615907-28617124	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZNF263	chr6:28616003-28617224	HEK293-T-REx	kidney:	n/a	n/a
21	ETS1	chr6:28615786-28616329	A549	lung:	n/a	n/a
22	CBX3	chr6:28615767-28616819	HCT-116	colon:	n/a	n/a
23	KAP1	chr6:28615780-28616928	U2OS	brain:	n/a	chr6:28616591-28616599
24	ATF2	chr6:28615836-28616394	H1-hESC	embryonic stem cell:	n/a	n/a
25	FOSL2	chr6:28615719-28616351	SK-N-SH	brain:	n/a	n/a
26	CBX3	chr6:28615902-28616412	K562	blood:	n/a	n/a
27	SREBP2	chr6:28614650-28616915	GM12878	blood:	n/a	n/a
28	POLR2A	chr6:28615891-28617224	SK-N-MC	brain:	n/a	n/a
29	TEAD4	chr6:28615859-28616503	SK-N-SH	brain:	n/a	n/a
30	MYC	chr6:28615953-28616448	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr6:28616314-28616394	Gliobla	brain:	n/a	n/a
32	RFX5	chr6:28615900-28616517	HepG2	liver:	n/a	n/a
33	TEAD4	chr6:28615669-28616599	HepG2	liver:	n/a	n/a
34	TEAD4	chr6:28616268-28616598	H1-hESC	embryonic stem cell:	n/a	n/a
35	STAT1	chr6:28615927-28616502	GM12878	blood:	n/a	n/a
36	TCF7L2	chr6:28615900-28616700	Hela-S3	cervix:	n/a	n/a
37	MBD4	chr6:28615701-28616417	HepG2	liver:	n/a	n/a
38	TEAD4	chr6:28615863-28616334	A549	lung:	n/a	n/a
39	CHD2	chr6:28615889-28616738	Hela-S3	cervix:	n/a	n/a
40	MAX	chr6:28615890-28616861	SK-N-SH	brain:	n/a	n/a
41	TEAD4	chr6:28615742-28616382	A549	lung:	n/a	n/a
42	MYBL2	chr6:28615712-28616849	HepG2	liver:	n/a	chr6:28616636-28616646
43	ARID3A	chr6:28615883-28616610	HepG2	liver:	n/a	n/a
44	CTCF	chr6:28616200-28616350	AG10803	skin:	n/a	n/a
45	TCF12	chr6:28615680-28616752	A549	lung:	n/a	n/a
46	MAX	chr6:28615824-28616864	HepG2	liver:	n/a	n/a
47	STAT3	chr6:28615881-28616393	Hela-S3	cervix:	n/a	n/a
48	MAX	chr6:28615857-28616848	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr6:28616250-28616722	Hela-S3	cervix:	n/a	n/a
50	SP4	chr6:28615777-28616377	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28579846..28585618-chr6:28609150..28616432,10	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SCAND3-1	chr6:28616063-28616428	XLOC_005663
2	lnc-SCAND3-1	chr6:28616086-28616843	NONHSAT108477

No data

Variant related genes	Relation type
ENSG00000272278	TF binding region
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10738069	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807034	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10807035	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10807037	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10807039	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12662929	0.88[EUR][1000 genomes]
rs16894169	0.90[EUR][1000 genomes]
rs16894171	0.87[EUR][1000 genomes]
rs16894191	0.89[EUR][1000 genomes]
rs2143766	0.83[ASN][1000 genomes]
rs392230	0.83[ASN][1000 genomes]
rs4713173	0.89[EUR][1000 genomes]
rs4947335	0.84[EUR][1000 genomes]
rs55963280	0.84[EUR][1000 genomes]
rs56227726	0.91[EUR][1000 genomes]
rs58490223	0.89[EUR][1000 genomes]
rs62402392	0.84[EUR][1000 genomes]
rs62402394	0.86[EUR][1000 genomes]
rs62406542	0.89[EUR][1000 genomes]
rs62406553	0.84[EUR][1000 genomes]
rs7746909	0.90[EUR][1000 genomes]
rs7748225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755705	0.84[ASN][1000 genomes]
rs7760867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767144	0.90[EUR][1000 genomes]
rs9295775	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs732395	BTN3A3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28615800-28616400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:28615800-28616400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr6:28615800-28616600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:28615800-28616600	Active TSS	HUVEC	blood vessel
5	chr6:28615800-28616600	Active TSS	NHEK	skin
6	chr6:28615800-28616800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:28615800-28616800	Active TSS	Ovary	ovary
8	chr6:28615800-28616800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr6:28615800-28616800	Bivalent/Poised TSS	HepG2	liver
10	chr6:28615800-28617000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:28615800-28617000	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:28615800-28617000	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr6:28615800-28617000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:28615800-28617000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:28615800-28617000	Active TSS	Brain Germinal Matrix	brain
16	chr6:28615800-28617000	Active TSS	Fetal Muscle Leg	muscle
17	chr6:28615800-28617000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
18	chr6:28615800-28617200	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr6:28615800-28617200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:28615800-28617200	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr6:28615800-28617200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:28615800-28617200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr6:28615800-28617200	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr6:28615800-28617200	Active TSS	Fetal Muscle Trunk	muscle
25	chr6:28615800-28617200	Active TSS	Rectal Smooth Muscle	rectum
26	chr6:28615800-28617200	Active TSS	Right Atrium	heart
27	chr6:28615800-28617200	Active TSS	HSMM	muscle
28	chr6:28615800-28617400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:28615800-28617400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr6:28615800-28617400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:28615800-28617400	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr6:28615800-28617400	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr6:28615800-28617400	Active TSS	Brain Hippocampus Middle	brain
34	chr6:28615800-28617600	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr6:28616000-28616400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
36	chr6:28616000-28616400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
37	chr6:28616000-28616400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr6:28616000-28616400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:28616000-28616600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:28616000-28616600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
41	chr6:28616000-28616600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
42	chr6:28616000-28616600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
43	chr6:28616000-28616600	Active TSS	Placenta	Placenta
44	chr6:28616000-28616600	Bivalent/Poised TSS	Psoas Muscle	Psoas
45	chr6:28616000-28616600	Active TSS	NH-A	brain
46	chr6:28616000-28616800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:28616000-28616800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
48	chr6:28616000-28616800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
49	chr6:28616000-28616800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:28616000-28616800	Flanking Bivalent TSS/Enh	Left Ventricle	heart

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