Variant report

Variant	rs3767862
Chromosome Location	chr1:212537702-212537703
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212531780..212534376-chr1:212536682..212539871,4	K562	blood:
2	chr1:212532088..212535630-chr1:212537355..212540816,4	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10019	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11119904	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12023488	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12024665	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12033246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12035647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036130	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12410664	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1389371	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs17042034	0.82[EUR][1000 genomes]
rs1774249	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1992643	0.96[CEU][hapmap];0.93[CHB][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2252044	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2298114	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs3099112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351380	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs351386	1.00[CEU][hapmap];0.84[TSI][hapmap]
rs351393	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351398	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs351401	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs351408	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs351417	0.81[EUR][1000 genomes]
rs3767861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3767863	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951588	1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4951589	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs518793	0.84[YRI][hapmap]
rs6659594	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs701905	0.86[YRI][hapmap];0.82[EUR][1000 genomes]
rs7415843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7519959	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521853	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7544225	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs792445	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs792447	0.86[YRI][hapmap]
rs792448	0.89[ASW][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap]

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	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3767862	LGTN	cis	cerebellum	SCAN
rs3767862	TMEM206	cis	cerebellum	SCAN
rs3767862	TMEM206	cis	Esophagus Mucosa	GTEx
rs3767862	TMEM206	cis	parietal	SCAN
rs3767862	NENF	cis	Esophagus Mucosa	GTEx
rs3767862	CD34	cis	cerebellum	SCAN
rs3767862	C1orf75	Cis_1M	lymphoblastoid	RTeQTL
rs3767862	SLC30A1	cis	cerebellum	SCAN
rs3767862	TMEM206	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
2	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
3	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:212513200-212541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:212513800-212540800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:212514400-212540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:212514800-212541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:212523600-212550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:212524000-212541800	Strong transcription	Fetal Thymus	thymus
18	chr1:212524400-212554600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:212525000-212541600	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr1:212525600-212541800	Strong transcription	Primary B cells from peripheral blood	blood
21	chr1:212525600-212545600	Strong transcription	Primary T cells from cord blood	blood
22	chr1:212526600-212540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:212526600-212540800	Weak transcription	Right Ventricle	heart
24	chr1:212526800-212538200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr1:212526800-212538400	Weak transcription	Aorta	Aorta
26	chr1:212526800-212540600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:212526800-212541200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr1:212526800-212549200	Weak transcription	Brain Germinal Matrix	brain
29	chr1:212526800-212550800	Weak transcription	HSMMtube	muscle
30	chr1:212526800-212582800	Weak transcription	Fetal Brain Male	brain
31	chr1:212527800-212538400	Weak transcription	Lung	lung
32	chr1:212528000-212540600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:212528400-212583000	Weak transcription	Fetal Kidney	kidney
34	chr1:212529000-212550800	Weak transcription	NHLF	lung
35	chr1:212529400-212539200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:212529400-212541200	Strong transcription	GM12878-XiMat	blood
37	chr1:212529400-212562400	Strong transcription	Dnd41	blood
38	chr1:212529600-212540400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:212529600-212541600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:212529800-212538800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr1:212529800-212540400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:212529800-212541000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr1:212529800-212541600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:212529800-212563200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:212530000-212540400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:212530200-212552600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:212531200-212542200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:212531400-212540400	Strong transcription	HUVEC	blood vessel
49	chr1:212531600-212538400	Weak transcription	Gastric	stomach
50	chr1:212531600-212538600	Weak transcription	Esophagus	oesophagus

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