Variant report

Variant	rs34781270
Chromosome Location	chr6:26593037-26593038
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:47)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:47 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:26592940-26593090	HepG2	liver:	n/a	n/a
2	CTCF	chr6:26592966-26593150	Gliobla	brain:	n/a	n/a
3	CTCF	chr6:26592980-26593130	HVMF	connective:	n/a	n/a
4	CTCF	chr6:26592960-26593110	HPAF	blood vessel:	n/a	n/a
5	CTCF	chr6:26592980-26593130	GM12878	blood:	n/a	n/a
6	CTCF	chr6:26592960-26593110	HCPEpiC	choroid plexus:	n/a	n/a
7	ARID3A	chr6:26592965-26593184	K562	blood:	n/a	n/a
8	CTCF	chr6:26593031-26593066	Medullo	brain:	n/a	n/a
9	MYC	chr6:26593003-26593181	K562	blood:	n/a	n/a
10	EBF1	chr6:26592990-26593162	GM12878	blood:	n/a	n/a
11	MAX	chr6:26592944-26593096	Hela-S3	cervix:	n/a	n/a
12	CTCF	chr6:26592920-26593070	AG04450	lung:	n/a	n/a
13	CTCF	chr6:26592980-26593130	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr6:26592895-26593223	GM12878	blood:	n/a	n/a
15	CTCF	chr6:26592885-26593238	K562	blood:	n/a	n/a
16	MAX	chr6:26592926-26593244	NB4	blood:	n/a	n/a
17	CTCF	chr6:26593000-26593150	HEK293	kidney:	n/a	n/a
18	CTCF	chr6:26592940-26593090	HRPEpiC	eye:	n/a	n/a
19	ZNF384	chr6:26592989-26593089	GM12878	blood:	n/a	n/a
20	SMC3	chr6:26592937-26593134	GM12878	blood:	n/a	n/a
21	CTCF	chr6:26592960-26593110	HRPEpiC	eye:	n/a	n/a
22	CTCF	chr6:26592940-26593090	HMF	breast:	n/a	n/a
23	CTCF	chr6:26592991-26593122	MCF-7	breast:	n/a	n/a
24	CTCF	chr6:26593020-26593170	HCPEpiC	choroid plexus:	n/a	n/a
25	ZNF384	chr6:26592951-26593193	K562	blood:	n/a	n/a
26	CTCF	chr6:26592960-26593110	AG10803	skin:	n/a	n/a
27	SMC3	chr6:26592956-26593151	Hela-S3	cervix:	n/a	n/a
28	MYC	chr6:26593035-26593217	NB4	blood:	n/a	n/a
29	CTCF	chr6:26592960-26593110	HBMEC	blood vessel:	n/a	n/a
30	CTCF	chr6:26592961-26593148	GM12878	blood:	n/a	n/a
31	CTCF	chr6:26593006-26593098	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr6:26593014-26593072	GM13977	blood:	n/a	n/a
33	RAD21	chr6:26592902-26593173	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr6:26593020-26593170	BJ	skin:	n/a	n/a
35	CTCF	chr6:26592940-26593090	K562	blood:	n/a	n/a
36	CTCF	chr6:26592920-26593070	HFF	foreskin:	n/a	n/a
37	RAD21	chr6:26592893-26593415	HCT-116	colon:	n/a	n/a
38	CTCF	chr6:26592940-26593090	HAc	cerebellar:	n/a	n/a
39	CTCF	chr6:26592980-26593130	BE2_C	brain:	n/a	n/a
40	CTCF	chr6:26592960-26593110	SK-N-SH_RA	brain:	n/a	n/a
41	RAD21	chr6:26592923-26593143	SK-N-SH_RA	brain:	n/a	n/a
42	CTCF	chr6:26592960-26593110	HA-sp	spinal cord:	n/a	n/a
43	CTCF	chr6:26592980-26593130	AG04449	skin:	n/a	n/a
44	CTCF	chr6:26592975-26593141	K562	blood:	n/a	n/a
45	CTCF	chr6:26592980-26593130	A549	lung:	n/a	n/a
46	CTCF	chr6:26592920-26593070	BE2_C	brain:	n/a	n/a
47	RAD21	chr6:26592895-26593161	SK-N-SH_RA	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26158173..26160142-chr6:26590992..26593219,3	K562	blood:
2	chr6:26269065..26272494-chr6:26592210..26596038,3	MCF-7	breast:
3	chr6:26581396..26586059-chr6:26589997..26593151,4	K562	blood:
4	chr6:26592995..26594553-chr6:26600001..26601767,2	K562	blood:

No data

Variant related genes	Relation type
ABT1	TF binding region
ENSG00000158373	Chromatin interaction
ENSG00000256018	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs13198716	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13212985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13220261	0.82[AFR][1000 genomes]
rs34148261	0.82[AMR][1000 genomes]
rs34246779	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35076545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35277236	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35400317	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35433030	1.00[AMR][1000 genomes]
rs35555795	0.82[AMR][1000 genomes]
rs36162392	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3734542	0.82[AFR][1000 genomes]
rs3734543	0.82[AFR][1000 genomes]
rs45527431	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66941101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71557340	1.00[AMR][1000 genomes]
rs72844462	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72845428	1.00[AMR][1000 genomes];0.88[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	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

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs34781270	BTN3A2	cis	Esophagus Mucosa	GTEx
rs34781270	BTN3A2	cis	Heart Left Ventricle	GTEx
rs34781270	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs34781270	BTN3A2	cis	Thyroid	GTEx
rs34781270	BTN3A2	cis	Stomach	GTEx
rs34781270	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs34781270	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs34781270	BTN3A2	cis	lung	GTEx
rs34781270	BTN3A2	cis	Muscle Skeletal	GTEx
rs34781270	BTN3A2	cis	Artery Aorta	GTEx
rs34781270	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs34781270	BTN3A2	cis	Whole Blood	GTEx
rs34781270	BTN3A2	cis	Nerve Tibial	GTEx
rs34781270	BTN3A2	cis	Artery Tibial	GTEx
rs34781270	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26592600-26593600	Enhancers	K562	blood
2	chr6:26593000-26593200	Bivalent Enhancer	NHDF-Ad	bronchial
3	chr6:26593000-26594000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:26593000-26598000	Active TSS	H1 Cell Line	embryonic stem cell
5	chr6:26593000-26598400	Active TSS	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links