Variant report

Variant	rs3816146
Chromosome Location	chr1:160511648-160511649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160509002..160516145-chr1:160518936..160522666,8	K562	blood:
2	chr1:160510384..160512674-chr1:160538457..160540708,2	K562	blood:
3	chr1:160510071..160512136-chr1:160549726..160552800,3	K562	blood:
4	chr1:160510180..160511755-chr1:160511798..160513582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1055880	0.84[CEU][hapmap]
rs1061217	0.92[ASW][hapmap];0.96[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10752638	0.83[EUR][1000 genomes]
rs10797073	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10797083	0.82[EUR][1000 genomes]
rs10908789	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10908794	0.83[EUR][1000 genomes]
rs10908796	0.83[EUR][1000 genomes]
rs11265442	0.96[CEU][hapmap];0.87[CHB][hapmap];0.83[EUR][1000 genomes]
rs11265452	0.88[CEU][hapmap]
rs1138323	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11583402	0.87[CEU][hapmap]
rs11585738	0.84[CEU][hapmap]
rs11590035	0.88[CEU][hapmap]
rs12144628	0.96[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12402879	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12728784	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12736781	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1394078	0.84[CEU][hapmap]
rs151607	0.88[CEU][hapmap]
rs1572382	0.96[CEU][hapmap];0.87[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1604783	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16832208	0.93[LWK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs16832283	0.88[CEU][hapmap]
rs17381453	0.84[CEU][hapmap]
rs17385407	0.84[CEU][hapmap]
rs1809963	0.88[CEU][hapmap]
rs1998651	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2025516	0.92[CEU][hapmap];0.81[JPT][hapmap]
rs2025517	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs2083128	0.87[CEU][hapmap]
rs2099604	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2753260	0.88[CEU][hapmap]
rs349249	0.87[ASN][1000 genomes]
rs3733264	0.84[CEU][hapmap]
rs3733265	0.84[CEU][hapmap]
rs3733266	0.84[CEU][hapmap]
rs3766385	0.84[CEU][hapmap]
rs3766387	0.87[CEU][hapmap]
rs3766388	0.88[CEU][hapmap]
rs3766389	0.84[CEU][hapmap]
rs4106115	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5002947	0.88[CEU][hapmap]
rs6427535	0.83[EUR][1000 genomes]
rs6656191	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6660233	0.85[CEU][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6668760	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6670721	0.88[CEU][hapmap]
rs6687641	0.88[CEU][hapmap]
rs6692382	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7521247	0.91[ASN][1000 genomes]
rs7528976	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7534679	0.85[EUR][1000 genomes]
rs7547054	0.88[CEU][hapmap]
rs7550771	0.88[CEU][hapmap]
rs912582	0.84[CEU][hapmap]
rs9726326	0.85[EUR][1000 genomes]
rs977019	0.92[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3816146	VANGL2	cis	cerebellum	SCAN
rs3816146	ADAMTS4	cis	cerebellum	SCAN
rs3816146	ADAMTS4	cis	parietal	SCAN
rs3816146	LRP1B	trans	parietal	SCAN
rs3816146	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs3816146	ATF6	cis	parietal	SCAN
rs3816146	OLFML2B	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160507600-160515400	Enhancers	Fetal Intestine Large	intestine
2	chr1:160507800-160515400	Enhancers	Fetal Intestine Small	intestine
3	chr1:160508400-160511800	Enhancers	Pancreas	Pancrea
4	chr1:160508400-160512000	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:160508400-160512000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:160508400-160512600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:160508400-160513200	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:160508600-160512200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:160508600-160513200	Enhancers	Liver	Liver
10	chr1:160508800-160512800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr1:160509400-160512000	Weak transcription	HMEC	breast
12	chr1:160509400-160512000	Weak transcription	NHEK	skin
13	chr1:160509600-160512200	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr1:160509800-160513200	Enhancers	Fetal Lung	lung
15	chr1:160510200-160511800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:160510200-160515000	Enhancers	Stomach Mucosa	stomach
17	chr1:160510200-160520400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:160510400-160512400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr1:160510400-160513200	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:160510600-160511800	Enhancers	Primary B cells from cord blood	blood
21	chr1:160510600-160511800	Enhancers	Colonic Mucosa	Colon
22	chr1:160510600-160512000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr1:160510600-160512200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr1:160510600-160512200	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:160510600-160512600	Enhancers	Primary T cells from cord blood	blood
26	chr1:160510600-160512600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr1:160510600-160515000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:160510600-160515600	Enhancers	Fetal Thymus	thymus
29	chr1:160510600-160516000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:160510600-160516200	Weak transcription	Placenta	Placenta
31	chr1:160510800-160511800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:160510800-160512000	Enhancers	Dnd41	blood
33	chr1:160510800-160512600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:160510800-160512800	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr1:160510800-160513000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr1:160510800-160513200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr1:160510800-160513200	Enhancers	Thymus	Thymus
38	chr1:160510800-160513200	Enhancers	GM12878-XiMat	blood
39	chr1:160510800-160513400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:160510800-160515400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:160511000-160515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:160511000-160515400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr1:160511200-160512800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:160511200-160513400	Enhancers	K562	blood
45	chr1:160511400-160511800	Enhancers	Gastric	stomach
46	chr1:160511400-160512000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr1:160511400-160512000	Enhancers	Small Intestine	intestine
48	chr1:160511400-160512400	Flanking Active TSS	A549	lung
49	chr1:160511400-160513000	Enhancers	HepG2	liver
50	chr1:160511600-160512400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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