Variant report

Variant	rs3774635
Chromosome Location	chr3:45986219-45986220
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	BCL3	chr3:45985998-45986337	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CXCR6	TF binding region

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1072755	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130080	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12630101	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635494	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635657	0.80[EUR][1000 genomes]
rs12639598	0.83[EUR][1000 genomes]
rs13066048	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091821	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13091979	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392291	0.81[ASN][1000 genomes]
rs1532071	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1552489	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1552490	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1601867	0.98[ASN][1000 genomes]
rs17078495	0.80[EUR][1000 genomes]
rs1994488	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1994489	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1994490	0.86[ASN][1000 genomes]
rs2054866	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2171530	0.81[ASN][1000 genomes]
rs2234358	0.97[ASN][1000 genomes]
rs2248228	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291470	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35465473	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733100	0.86[ASN][1000 genomes]
rs3733103	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774634	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774639	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796373	0.82[ASN][1000 genomes]
rs3796375	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821884	0.82[ASN][1000 genomes]
rs4535265	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682799	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4682800	0.96[ASN][1000 genomes]
rs4683148	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683149	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683152	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683154	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683156	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683157	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67044455	0.80[EUR][1000 genomes]
rs6778896	0.83[EUR][1000 genomes]
rs7129	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs737452	0.80[EUR][1000 genomes]
rs751552	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs751553	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311380	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs936938	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs936939	0.81[ASN][1000 genomes]
rs9824253	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9831315	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];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	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:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45958800-45988000	Weak transcription	HUVEC	blood vessel
2	chr3:45959400-46009800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:45970200-45988200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:45972800-45988600	Weak transcription	Small Intestine	intestine
5	chr3:45973400-45986400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
8	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
9	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
10	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:45978400-45986600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:45979000-45987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:45979000-45988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
19	chr3:45979200-45987200	Weak transcription	Colonic Mucosa	Colon
20	chr3:45979200-45987800	Weak transcription	Brain Anterior Caudate	brain
21	chr3:45979200-45987800	Weak transcription	HepG2	liver
22	chr3:45979200-45988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:45980800-45986800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:45980800-45988000	Weak transcription	NH-A	brain
25	chr3:45980800-45989200	Weak transcription	Fetal Brain Male	brain
26	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:45981000-45986400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:45981000-45986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:45981000-45986600	Weak transcription	Brain Angular Gyrus	brain
30	chr3:45981000-45987800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:45981000-45988000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:45981000-45988000	Weak transcription	NHDF-Ad	bronchial
33	chr3:45981000-45988000	Weak transcription	Osteobl	bone
34	chr3:45981000-45988200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr3:45981000-45990400	Weak transcription	Fetal Brain Female	brain
36	chr3:45981000-45993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:45981000-45999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr3:45981200-45987400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:45981200-45987600	Weak transcription	NHLF	lung
40	chr3:45981200-45987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:45981200-45988000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr3:45981200-45988000	Weak transcription	GM12878-XiMat	blood
43	chr3:45981400-45986600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:45981400-45987600	Weak transcription	HSMM	muscle
45	chr3:45981400-45988400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:45981600-45987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
48	chr3:45982000-45987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr3:45982000-45987400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr3:45982000-45987800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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