Variant report

Variant	rs35589403
Chromosome Location	chr6:27219491-27219492
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:195)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:195 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr6:27219244-27220013	A549	lung:	n/a	chr6:27219294-27219304 chr6:27219294-27219303 chr6:27219293-27219305 chr6:27219295-27219304 chr6:27219293-27219305 chr6:27219295-27219304
2	MAX	chr6:27218573-27219998	K562	blood:	n/a	n/a
3	YY1	chr6:27218655-27220079	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:27219013-27219849	GM15510	blood:	n/a	n/a
5	YY1	chr6:27218678-27219909	K562	blood:	n/a	n/a
6	CBX3	chr6:27218575-27220172	K562	blood:	n/a	n/a
7	TEAD4	chr6:27218428-27220231	K562	blood:	n/a	n/a
8	TEAD4	chr6:27219408-27220022	K562	blood:	n/a	n/a
9	POLR2A	chr6:27219384-27220032	HCT-116	colon:	n/a	n/a
10	POLR2A	chr6:27219371-27219894	GM12878	blood:	n/a	n/a
11	YY1	chr6:27219035-27219940	K562	blood:	n/a	n/a
12	ZEB1	chr6:27219460-27219833	GM12878	blood:	n/a	n/a
13	ZMIZ1	chr6:27219422-27219975	K562	blood:	n/a	n/a
14	MAX	chr6:27218549-27220163	MCF-7	breast:	n/a	n/a
15	MAX	chr6:27218798-27220196	A549	lung:	n/a	n/a
16	PML	chr6:27219378-27220127	GM12878	blood:	n/a	n/a
17	PBX3	chr6:27219460-27219922	SK-N-SH	brain:	n/a	n/a
18	ZBTB7A	chr6:27218403-27219867	K562	blood:	n/a	n/a
19	MAX	chr6:27218635-27220214	K562	blood:	n/a	n/a
20	MYC	chr6:27219488-27219911	MCF-7	breast:	n/a	n/a
21	JUND	chr6:27218688-27219960	K562	blood:	n/a	n/a
22	E2F6	chr6:27218276-27219991	K562	blood:	n/a	chr6:27218683-27218695
23	POLR2A	chr6:27218606-27219930	K562	blood:	n/a	n/a
24	TCF12	chr6:27219341-27220170	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr6:27219490-27219794	IMR90	lung:	n/a	n/a
26	RUNX3	chr6:27219367-27220031	GM12878	blood:	n/a	n/a
27	ZNF143	chr6:27219463-27220107	K562	blood:	n/a	n/a
28	POLR2A	chr6:27218935-27219970	A549	lung:	n/a	n/a
29	CTCF	chr6:27219385-27219904	K562	blood:	n/a	n/a
30	E2F6	chr6:27219485-27219665	K562	blood:	n/a	n/a
31	CTCF	chr6:27219480-27219832	T-47D	breast:	n/a	n/a
32	CTCFL	chr6:27219370-27219787	K562	blood:	n/a	n/a
33	POLR2A	chr6:27218790-27219909	MCF10A-Er-Src	breast:	n/a	n/a
34	CTCF	chr6:27219458-27219810	Fibrobl	skin:	n/a	n/a
35	CCNT2	chr6:27219398-27219945	K562	blood:	n/a	n/a
36	POLR2A	chr6:27218718-27219991	MCF-7	breast:	n/a	n/a
37	E2F6	chr6:27219489-27220061	A549	lung:	n/a	n/a
38	CTCF	chr6:27219357-27220348	A549	lung:	n/a	n/a
39	POLR2A	chr6:27218933-27219911	K562	blood:	n/a	n/a
40	SP1	chr6:27219378-27220017	A549	lung:	n/a	n/a
41	GABPA	chr6:27219425-27220004	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr6:27218937-27219856	K562	blood:	n/a	n/a
43	POLR2A	chr6:27218696-27220117	SK-N-MC	brain:	n/a	n/a
44	CTCF	chr6:27219428-27220088	K562	blood:	n/a	n/a
45	CREB1	chr6:27219386-27220025	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr6:27219228-27219891	A549	lung:	n/a	n/a
47	ZBTB7A	chr6:27218535-27219894	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr6:27218749-27220114	HCT-116	colon:	n/a	n/a
49	GABPA	chr6:27218733-27220161	MCF-7	breast:	n/a	n/a
50	RAD21	chr6:27219466-27219984	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27110323..27115581-chr6:27216717..27220429,5	K562	blood:
2	chr6:26285137..26286889-chr6:27219184..27221854,2	MCF-7	breast:
3	chr6:27099473..27102319-chr6:27217669..27219889,2	K562	blood:
4	chr6:27111807..27118148-chr6:27215986..27222524,9	K562	blood:
5	chr6:27217680..27220381-chr6:27773874..27775997,2	K562	blood:
6	chr6:27217585..27220597-chr6:27438809..27440860,3	K562	blood:
7	chr6:27218208..27219861-chr6:27859108..27862899,3	K562	blood:
8	chr1:110576957..110577749-chr6:27219027..27219766,2	HCT-116	colon:

No data

Variant related genes	Relation type
PRSS16	TF binding region
ENSG00000196331	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000096654	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000143093	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13211901	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36034627	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3800307	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6938200	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv3366700	chr6:27218098-27220596	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs35589403	BTN3A2	cis	Whole Blood	GTEx
rs35589403	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs35589403	BTN3A2	cis	lung	GTEx
rs35589403	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs35589403	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27217800-27220200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:27218000-27220000	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr6:27218000-27220200	Active TSS	H9 Cell Line	embryonic stem cell
4	chr6:27218000-27220200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
5	chr6:27218200-27219800	Bivalent/Poised TSS	Aorta	Aorta
6	chr6:27218200-27220000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:27218200-27220000	Active TSS	A549	lung
8	chr6:27218200-27220200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:27218200-27220200	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr6:27218200-27220200	Active TSS	Duodenum Mucosa	Duodenum
11	chr6:27218200-27220400	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:27218400-27219800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
13	chr6:27218400-27219800	Active TSS	Gastric	stomach
14	chr6:27218400-27219800	Active TSS	Pancreas	Pancrea
15	chr6:27218400-27220000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:27218400-27220000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:27218400-27220000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
18	chr6:27218400-27220000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:27218400-27220000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
20	chr6:27218400-27220200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr6:27218400-27220200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:27218400-27220200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
23	chr6:27218400-27220400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:27218400-27220600	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:27218600-27219600	Active TSS	Right Atrium	heart
26	chr6:27218600-27219800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
27	chr6:27218600-27219800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr6:27218600-27219800	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr6:27218600-27219800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr6:27218600-27219800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
31	chr6:27218600-27219800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
32	chr6:27218600-27219800	Bivalent/Poised TSS	Small Intestine	intestine
33	chr6:27218600-27219800	Bivalent/Poised TSS	HepG2	liver
34	chr6:27218600-27219800	Active TSS	K562	blood
35	chr6:27218600-27220000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr6:27218600-27220000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:27218600-27220000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:27218600-27220000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:27218600-27220000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:27218600-27220000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:27218600-27220000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
42	chr6:27218600-27220000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
43	chr6:27218600-27220000	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr6:27218600-27220000	Bivalent/Poised TSS	Stomach Mucosa	stomach
45	chr6:27218600-27220000	Active TSS	GM12878-XiMat	blood
46	chr6:27218600-27220000	Active TSS	NHEK	skin
47	chr6:27218600-27220200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:27218600-27220200	Active TSS	HUES64 Cell Line	embryonic stem cell
49	chr6:27218800-27219600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
50	chr6:27218800-27219600	Bivalent/Poised TSS	Fetal Lung	lung

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