Variant report

Variant	rs12635657
Chromosome Location	chr3:46031029-46031030
allele	C/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	STAT3	chr3:46030999-46031130	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr3:46030960-46031149	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46023503..46025098-chr3:46030445..46033156,2	K562	blood:
2	chr3:45998846..46001598-chr3:46029585..46032027,2	K562	blood:

Variant related genes	Relation type
FYCO1	TF binding region
ENSG00000163820	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1072755	1.00[CEU][hapmap]
rs11130080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12485978	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs12495073	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12630101	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12635494	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12639598	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13060901	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs13066048	1.00[CEU][hapmap]
rs13073861	0.85[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs1392290	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1392291	0.91[ASN][1000 genomes]
rs1491959	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1500005	0.80[ASN][1000 genomes]
rs1546077	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs1552489	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1552490	0.80[EUR][1000 genomes]
rs1601867	0.81[ASN][1000 genomes]
rs17078495	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994488	0.80[EUR][1000 genomes]
rs1994490	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2054866	1.00[CEU][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2131091	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2234358	0.81[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs2373154	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs28808964	0.84[AFR][1000 genomes];0.88[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];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3733100	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3733103	0.90[CEU][hapmap]
rs3774634	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3774635	0.80[EUR][1000 genomes]
rs3774639	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3796375	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821883	0.83[ASN][1000 genomes]
rs3821884	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3851347	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs4234452	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4333119	0.80[ASN][1000 genomes]
rs4535265	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4682800	0.84[JPT][hapmap]
rs4682810	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4683148	0.95[CEU][hapmap]
rs4683156	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];1.00[YRI][hapmap];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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764042	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6778896	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780163	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6781668	0.83[ASN][1000 genomes]
rs6795629	0.81[CHB][hapmap]
rs6805094	0.83[ASN][1000 genomes]
rs6809381	0.85[CHB][hapmap]
rs7129	0.90[CEU][hapmap]
rs730983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751552	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs751553	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7616464	0.80[ASN][1000 genomes]
rs7623460	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7643426	0.84[CHB][hapmap]
rs931704	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs9824253	0.80[EUR][1000 genomes]
rs9824886	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs9831315	0.95[CEU][hapmap]
rs9849015	0.81[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	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	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
4	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
rs12635657	CXCR6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46010200-46033000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46013600-46034000	Genic enhancers	Fetal Thymus	thymus
3	chr3:46020000-46034200	Genic enhancers	Dnd41	blood
4	chr3:46021400-46036200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:46021600-46034000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:46025000-46031600	Weak transcription	Fetal Kidney	kidney
7	chr3:46025200-46031800	Enhancers	Right Atrium	heart
8	chr3:46025600-46032400	Enhancers	Stomach Mucosa	stomach
9	chr3:46025600-46033000	Enhancers	Right Ventricle	heart
10	chr3:46025800-46031200	Enhancers	HSMMtube	muscle
11	chr3:46026000-46031800	Enhancers	NHDF-Ad	bronchial
12	chr3:46026200-46031800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr3:46026200-46032000	Enhancers	Ovary	ovary
14	chr3:46026200-46032000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr3:46026200-46032000	Enhancers	NHLF	lung
16	chr3:46026400-46031400	Enhancers	HSMM	muscle
17	chr3:46026400-46031600	Enhancers	Fetal Intestine Large	intestine
18	chr3:46026400-46031800	Enhancers	Fetal Muscle Leg	muscle
19	chr3:46026400-46033800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:46026400-46034600	Genic enhancers	Primary T cells fromperipheralblood	blood
21	chr3:46026600-46031400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:46026600-46031400	Enhancers	Lung	lung
23	chr3:46026600-46031600	Enhancers	Pancreas	Pancrea
24	chr3:46026600-46031800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:46026600-46032200	Enhancers	Liver	Liver
26	chr3:46026600-46032200	Enhancers	Duodenum Mucosa	Duodenum
27	chr3:46026600-46033000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:46026600-46033000	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:46026600-46033000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr3:46026600-46036200	Enhancers	Left Ventricle	heart
31	chr3:46026800-46032800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:46026800-46033400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:46026800-46033600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:46026800-46033800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:46026800-46035600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:46027000-46031400	Enhancers	NH-A	brain
37	chr3:46027000-46032200	Enhancers	Psoas Muscle	Psoas
38	chr3:46027200-46031400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:46027200-46031800	Enhancers	Gastric	stomach
40	chr3:46027200-46033400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:46027200-46036000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:46027400-46031200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:46027400-46031400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr3:46027400-46031600	Enhancers	Brain Anterior Caudate	brain
45	chr3:46027400-46031800	Enhancers	Esophagus	oesophagus
46	chr3:46027400-46032000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:46027400-46032000	Enhancers	HMEC	breast
48	chr3:46027400-46032800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:46027600-46031400	Enhancers	Small Intestine	intestine
50	chr3:46027600-46033000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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