Variant report

Variant	rs6446274
Chromosome Location	chr3:49465601-49465602
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	EBF1	chr3:49465547-49465909	GM12878	blood:	n/a	n/a
2	JUN	chr3:49465575-49465962	K562	blood:	n/a	chr3:49465741-49465749 chr3:49465742-49465749

No.	Distal block	Cell Line	Cell type
1	chr3:49376764..49379634-chr3:49465144..49467494,3	MCF-7	breast:
2	chr3:49375307..49378756-chr3:49465334..49469314,4	K562	blood:
3	chr3:49463180..49464811-chr3:49464830..49467753,3	K562	blood:
4	chr3:49457686..49462880-chr3:49464384..49468098,7	MCF-7	breast:
5	chr3:49460720..49464051-chr3:49464777..49467713,3	MCF-7	breast:
6	chr3:49447469..49451415-chr3:49463621..49468909,12	K562	blood:

Variant related genes	Relation type
NICN1	TF binding region
ENSG00000145022	Chromatin interaction
ENSG00000145020	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000235261	Chromatin interaction
ENSG00000067560	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10640	0.87[ASN][1000 genomes]
rs10865955	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11130192	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130193	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130194	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11130196	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130199	0.82[EUR][1000 genomes]
rs11706370	0.87[ASN][1000 genomes]
rs11715915	0.87[ASN][1000 genomes]
rs11922013	0.87[ASN][1000 genomes]
rs12489092	0.80[EUR][1000 genomes]
rs13096760	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1464566	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1464567	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1464568	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1568661	0.82[EUR][1000 genomes]
rs1568662	0.81[EUR][1000 genomes]
rs17595772	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17650792	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2117939	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2878298	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34937635	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35701831	0.83[EUR][1000 genomes]
rs3870337	0.80[EUR][1000 genomes]
rs3870338	0.80[EUR][1000 genomes]
rs3877784	0.83[EUR][1000 genomes]
rs3924462	0.83[EUR][1000 genomes]
rs4459909	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4563439	0.86[EUR][1000 genomes]
rs4855842	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4855843	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4855855	0.81[EUR][1000 genomes]
rs4855859	0.83[EUR][1000 genomes]
rs4855861	0.81[EUR][1000 genomes]
rs4855864	0.82[EUR][1000 genomes]
rs4855866	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4855873	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4855877	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955412	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4955438	0.86[EUR][1000 genomes]
rs55957735	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59152804	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62259939	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62259942	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6446272	0.87[ASN][1000 genomes]
rs6773518	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779524	0.87[ASN][1000 genomes]
rs6784820	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6792911	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6797765	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6997	0.87[ASN][1000 genomes]
rs7371895	0.81[EUR][1000 genomes]
rs7373849	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7621003	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7631908	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7637999	0.83[EUR][1000 genomes]
rs7643586	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7643845	0.82[EUR][1000 genomes]
rs7645445	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs885592	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9814873	0.85[ASN][1000 genomes]
rs9859556	0.83[ASN][1000 genomes]
rs9871380	0.87[ASN][1000 genomes]
rs9878943	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv963482	chr3:49459177-49486938	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6446274	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6446274	WDR6	cis	Whole Blood	GTEx
rs6446274	WDR6	cis	Adipose Subcutaneous	GTEx
rs6446274	WDR6	cis	Muscle Skeletal	GTEx
rs6446274	WDR6	cis	Artery Tibial	GTEx
rs6446274	WDR6	cis	Nerve Tibial	GTEx
rs6446274	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6446274	WDR6	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
2	chr3:49455600-49466200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr3:49457400-49466000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:49459200-49466200	Weak transcription	HUVEC	blood vessel
5	chr3:49459400-49465800	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:49459600-49466200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:49459600-49466200	Weak transcription	HMEC	breast
8	chr3:49460200-49466000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:49460400-49465800	Weak transcription	Brain Angular Gyrus	brain
10	chr3:49460400-49465800	Weak transcription	Right Atrium	heart
11	chr3:49460400-49466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:49460600-49465800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:49460600-49465800	Weak transcription	Brain Substantia Nigra	brain
14	chr3:49460600-49465800	Weak transcription	Fetal Brain Male	brain
15	chr3:49460600-49466000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:49460600-49466000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:49460600-49466000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:49460600-49466000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:49460600-49466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:49460600-49466200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:49460600-49466200	Weak transcription	Small Intestine	intestine
22	chr3:49460600-49466200	Weak transcription	Stomach Mucosa	stomach
23	chr3:49460600-49466200	Weak transcription	HSMM	muscle
24	chr3:49460600-49466200	Weak transcription	Osteobl	bone
25	chr3:49460800-49465800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:49460800-49466000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:49460800-49466000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr3:49460800-49466000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:49460800-49466200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:49460800-49466200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:49460800-49466200	Weak transcription	Fetal Heart	heart
32	chr3:49460800-49466200	Weak transcription	Fetal Kidney	kidney
33	chr3:49460800-49466200	Weak transcription	HSMMtube	muscle
34	chr3:49462000-49465800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:49462200-49465800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:49462400-49465800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:49462600-49466200	Weak transcription	NHLF	lung
38	chr3:49462800-49466000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:49463200-49466200	Weak transcription	Left Ventricle	heart
40	chr3:49463600-49465800	Weak transcription	Brain Germinal Matrix	brain
41	chr3:49463600-49466200	Weak transcription	Primary T cells from cord blood	blood
42	chr3:49463600-49466200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:49463600-49466200	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr3:49463800-49465800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:49463800-49465800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:49463800-49465800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:49463800-49465800	Weak transcription	Primary B cells from cord blood	blood
48	chr3:49463800-49465800	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:49463800-49465800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:49463800-49465800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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