Variant report

Variant	rs41289608
Chromosome Location	chr3:45928138-45928139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr3:45927616-45928442	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:45927852-45928239	GM12878	blood:	n/a	n/a
3	MTA3	chr3:45927493-45929246	GM12878	blood:	n/a	n/a
4	MTA3	chr3:45927578-45929612	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:45927713-45928206	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:45927784-45928209	GM12891	blood:	n/a	n/a
7	PML	chr3:45927287-45928625	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:45928137-45928187	PFSK-1	brain:	n/a
2	chr3:45928137-45928187	MCF10A-Er-Src	breast:	n/a
3	chr3:45928137-45928187	Caco-2	colon:	n/a
4	chr3:45928137-45928187	PrEC	prostate:	n/a
5	chr3:45928137-45928187	Hepatocyte	liver:	n/a
6	chr3:45928137-45928187	HRPEpiC	eye:	n/a
7	chr3:45928137-45928187	SK-N-MC	brain:	n/a
8	chr3:45928137-45928187	SKMC	muscle:	n/a
9	chr3:45928137-45928187	NH-A	brain:	n/a
10	chr3:45928137-45928187	HRCEpiC	kidney:	n/a
11	chr3:45928137-45928187	IMR90	lung:	fetal
12	chr3:45928137-45928187	HUVEC	blood vessel:	n/a
13	chr3:45928137-45928187	U87	brain:	n/a
14	chr3:45928137-45928187	SK-N-SH_RA	brain:	n/a
15	chr3:45928137-45928187	HCPEpiC	choroid plexus:	n/a
16	chr3:45928137-45928187	A549	lung:	n/a
17	chr3:45928137-45928187	HepG2	liver:	n/a
18	chr3:45928137-45928187	GM12878	blood:	n/a
19	chr3:45928137-45928187	HAEpiC	amniotic membrane:	n/a
20	chr3:45928137-45928187	GM06990	blood:	n/a
21	chr3:45928137-45928187	HIPEpiC	eye:	n/a
22	chr3:45928137-45928187	AoSMC	blood vessel:	n/a
23	chr3:45928137-45928187	RPTEC	kidney:	n/a
24	chr3:45928137-45928187	HL-60	blood:	n/a
25	chr3:45928137-45928187	HNPCEpiC	eye:	n/a
26	chr3:45928137-45928187	BJ	skin:	n/a
27	chr3:45928137-45928187	T-47D	breast:	n/a
28	chr3:45928137-45928187	AG09319	gingival:	n/a
29	chr3:45928137-45928187	HCT-116	colon:	n/a
30	chr3:45928137-45928187	CMK	blood:	n/a
31	chr3:45928137-45928187	NT2-D1	testis:	n/a
32	chr3:45928137-45928187	K562	blood:	n/a
33	chr3:45928137-45928187	HMEC	breast:	n/a
34	chr3:45928137-45928187	AG04449	skin:	fetal
35	chr3:45928137-45928187	HEK293	kidney:	embryo
36	chr3:45928137-45928187	SK-N-SH	brain:	n/a
37	chr3:45928137-45928187	Jurkat	blood:	n/a
38	chr3:45928137-45928187	AG09309	skin:	n/a
39	chr3:45928137-45928187	AG04450	lung:	fetal
40	chr3:45928137-45928187	GM19239	blood:	n/a
41	chr3:45928137-45928187	BE2_C	brain:	n/a
42	chr3:45928137-45928187	HCF	heart:	n/a
43	chr3:45928137-45928187	HRE	kidney:	n/a
44	chr3:45928137-45928187	MCF-7	breast:	n/a
45	chr3:45928137-45928187	GM12891	blood:	n/a
46	chr3:45928137-45928187	HEEpiC	esophagus:	n/a
47	chr3:45928137-45928187	NB4	blood:	n/a
48	chr3:45928137-45928187	NHDF-neo	bronchial:	n/a
49	chr3:45928137-45928187	H1-hESC	embryonic stem cell:	embryo
50	chr3:45928137-45928187	SAEC	small airway:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CXCR6-1	chr3:45928054-45928147	NONHSAT089422
2	lnc-CXCR6-1	chr3:45928002-45928147	NONHSAT089421

No data

Variant related genes	Relation type
ENSG00000236930	TF binding region
ENSG00000236930	CpG island

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17078408	0.81[EUR][1000 genomes]
rs2373086	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775854	0.81[EUR][1000 genomes]
rs7648467	0.81[EUR][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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv834678	chr3:45804294-46010256	Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45923400-45930000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:45923400-45932000	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:45923400-45948200	Weak transcription	Right Atrium	heart
4	chr3:45923600-45930200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:45925200-45949600	Weak transcription	Pancreas	Pancrea
6	chr3:45925600-45947800	Genic enhancers	Dnd41	blood
7	chr3:45926600-45932600	Enhancers	GM12878-XiMat	blood
8	chr3:45927400-45928200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:45927400-45928200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:45927400-45928200	Enhancers	Primary T cells from cord blood	blood
11	chr3:45927400-45928400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr3:45927400-45928600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
13	chr3:45927800-45928200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr3:45927800-45928400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr3:45927800-45928400	Transcr. at gene 5' and 3'	Thymus	Thymus
16	chr3:45927800-45936400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:45928000-45928200	Enhancers	Primary B cells from peripheral blood	blood
18	chr3:45928000-45928200	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr3:45928000-45928600	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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