Variant report

Variant	rs17078495
Chromosome Location	chr3:46026641-46026642
allele	G/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	HNF4A	chr3:46026502-46026710	HepG2	liver:	n/a	chr3:46026593-46026605 chr3:46026592-46026606 chr3:46026592-46026606 chr3:46026592-46026605 chr3:46026593-46026605 chr3:46026591-46026606 chr3:46026593-46026605

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46026501..46029475-chr3:46032165..46035137,4	MCF-7	breast:

Variant related genes	Relation type
FYCO1	TF binding region

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11130080	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12495073	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12630101	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635494	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12635657	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639598	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060901	0.83[ASN][1000 genomes]
rs1392290	0.82[ASN][1000 genomes]
rs1392291	0.91[ASN][1000 genomes]
rs1500005	0.80[ASN][1000 genomes]
rs1552489	0.80[EUR][1000 genomes]
rs1552490	0.80[EUR][1000 genomes]
rs1601867	0.81[ASN][1000 genomes]
rs1994488	0.80[EUR][1000 genomes]
rs1994490	0.93[ASN][1000 genomes]
rs2054866	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2234358	0.81[ASN][1000 genomes]
rs28808964	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34381514	0.80[ASN][1000 genomes]
rs35465473	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35537559	1.00[ASN][1000 genomes]
rs3733097	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733100	0.93[ASN][1000 genomes]
rs3774634	0.80[EUR][1000 genomes]
rs3774635	0.80[EUR][1000 genomes]
rs3774639	0.81[EUR][1000 genomes]
rs3796375	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821883	0.83[ASN][1000 genomes]
rs3821884	0.93[ASN][1000 genomes]
rs3851347	0.84[ASN][1000 genomes]
rs4234452	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4333119	0.80[ASN][1000 genomes]
rs4683156	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683157	0.80[ASN][1000 genomes]
rs59226168	1.00[ASN][1000 genomes]
rs60539039	0.89[ASN][1000 genomes]
rs62242796	1.00[ASN][1000 genomes]
rs67044455	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764042	0.83[ASN][1000 genomes]
rs6778896	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6781668	0.83[ASN][1000 genomes]
rs6805094	0.83[ASN][1000 genomes]
rs730983	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737452	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751552	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751553	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616464	0.80[ASN][1000 genomes]
rs7623460	0.83[ASN][1000 genomes]
rs931704	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936938	0.80[EUR][1000 genomes]
rs9824253	0.80[EUR][1000 genomes]
rs9849015	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17078495	CXCR6	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr3:46002600-46027200	Weak transcription	A549	lung
7	chr3:46009000-46027800	Weak transcription	Fetal Brain Male	brain
8	chr3:46010200-46027000	Weak transcription	Fetal Brain Female	brain
9	chr3:46010200-46029600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
12	chr3:46015600-46027200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:46015800-46026800	Strong transcription	Brain Hippocampus Middle	brain
14	chr3:46015800-46027600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:46016200-46027800	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr3:46018800-46026800	Strong transcription	Primary hematopoietic stem cells	blood
17	chr3:46019200-46026800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:46019400-46030000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
20	chr3:46020400-46027200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:46020800-46027000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:46021400-46026800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr3:46021400-46028200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:46022400-46027400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:46022600-46027600	Strong transcription	GM12878-XiMat	blood
28	chr3:46022600-46028000	Strong transcription	Primary B cells from cord blood	blood
29	chr3:46022800-46027000	Strong transcription	Spleen	Spleen
30	chr3:46022800-46027200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:46023000-46027400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:46023000-46029800	Strong transcription	Primary T cells from cord blood	blood
33	chr3:46023200-46026800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:46023200-46027000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:46023200-46027600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:46023200-46028200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:46023600-46027200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:46023600-46027200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:46023600-46027400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr3:46023800-46026800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:46024200-46027000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:46024200-46027400	Weak transcription	HMEC	breast
43	chr3:46024600-46027400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr3:46024800-46026800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr3:46024800-46027200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:46025000-46029400	Genic enhancers	Fetal Intestine Small	intestine
47	chr3:46025000-46031600	Weak transcription	Fetal Kidney	kidney
48	chr3:46025200-46027000	Genic enhancers	Placenta	Placenta
49	chr3:46025200-46031800	Enhancers	Right Atrium	heart
50	chr3:46025400-46027000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links