Variant report

Variant	rs3774634
Chromosome Location	chr3:45986442-45986443
allele	C/G
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	POLR2A	chr3:45986410-45986943	K562	blood:	n/a	n/a

Variant related genes	Relation type
CXCR6	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1072755	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11130080	0.96[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12495073	0.92[CEU][hapmap]
rs12630101	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12635494	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12635657	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12639598	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13066048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13073861	0.85[CEU][hapmap]
rs13091821	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13091979	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392291	0.81[ASN][1000 genomes]
rs1532071	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1552489	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1552490	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1601867	0.98[ASN][1000 genomes]
rs17078449	0.84[CHB][hapmap]
rs17078495	0.80[EUR][1000 genomes]
rs1994488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1994489	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1994490	0.86[ASN][1000 genomes]
rs2054866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2131091	0.84[CEU][hapmap]
rs2171530	0.81[ASN][1000 genomes]
rs2234358	1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs2248228	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291470	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2373154	0.92[CEU][hapmap]
rs35465473	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733100	0.86[ASN][1000 genomes]
rs3733103	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774635	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3774638	0.90[CHB][hapmap]
rs3774639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796373	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs3796375	0.96[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821884	0.82[ASN][1000 genomes]
rs4535265	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682799	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4682800	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4683147	0.83[CEU][hapmap]
rs4683148	0.96[CEU][hapmap];0.85[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4683149	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683152	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4683154	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683156	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683157	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[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	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs730983	0.96[CEU][hapmap]
rs737452	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs751552	0.96[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs751553	0.96[CEU][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9311380	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs936938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs936939	0.89[CHB][hapmap];0.81[ASN][1000 genomes]
rs9824253	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9831315	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[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:125 , 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	chr3:45973800-45988000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:45973800-45991400	Weak transcription	Brain Germinal Matrix	brain
7	chr3:45974400-45988000	Weak transcription	Fetal Kidney	kidney
8	chr3:45977400-45987000	Weak transcription	Fetal Lung	lung
9	chr3:45977400-45988000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:45977600-45987600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:45978000-45988000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:45978200-45988200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:45978400-45986600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:45978800-45994400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:45979000-45987200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:45979000-45988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:45979000-45993000	Weak transcription	Stomach Mucosa	stomach
18	chr3:45979200-45987200	Weak transcription	Colonic Mucosa	Colon
19	chr3:45979200-45987800	Weak transcription	Brain Anterior Caudate	brain
20	chr3:45979200-45987800	Weak transcription	HepG2	liver
21	chr3:45979200-45988200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:45980800-45986800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:45980800-45988000	Weak transcription	NH-A	brain
24	chr3:45980800-45989200	Weak transcription	Fetal Brain Male	brain
25	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:45981000-45986600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:45981000-45986600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:45981000-45987800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:45981000-45988000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:45981000-45988000	Weak transcription	NHDF-Ad	bronchial
31	chr3:45981000-45988000	Weak transcription	Osteobl	bone
32	chr3:45981000-45988200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:45981000-45990400	Weak transcription	Fetal Brain Female	brain
34	chr3:45981000-45993400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:45981000-45999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:45981200-45987400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:45981200-45987600	Weak transcription	NHLF	lung
38	chr3:45981200-45987800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:45981200-45988000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:45981200-45988000	Weak transcription	GM12878-XiMat	blood
41	chr3:45981400-45986600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:45981400-45987600	Weak transcription	HSMM	muscle
43	chr3:45981400-45988400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr3:45981600-45987800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
46	chr3:45982000-45987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:45982000-45987400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:45982000-45987800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:45982000-45988000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr3:45982000-45988400	Weak transcription	Colon Smooth Muscle	Colon

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