Variant report

Variant	rs3766615
Chromosome Location	chr1:210018736-210018737
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210002486..210004655-chr1:210015863..210018980,3	K562	blood:
2	chr1:210017330..210020093-chr1:210023208..210026466,3	K562	blood:
3	chr1:210018303..210020361-chr1:210546029..210548987,2	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10127937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10218448	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10489344	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119354	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582607	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11584081	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590807	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11810091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12401430	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12403006	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12404886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17317580	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17389541	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2013196	0.83[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28601717	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34743335	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3753510	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3753513	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41274838	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4240837	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56071308	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56268268	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61820635	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699507	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs7526313	0.82[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7544804	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7546104	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932334	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3766615	ETNK2	cis	cerebellum	SCAN
rs3766615	IKBKE	cis	parietal	SCAN
rs3766615	HHAT	cis	parietal	SCAN
rs3766615	IRF6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210001800-210025000	Weak transcription	Stomach Mucosa	stomach
2	chr1:210001800-210034000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:210002000-210023800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:210002400-210032000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:210003200-210027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:210003200-210028600	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr1:210003200-210029400	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:210003400-210028000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:210003400-210028400	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:210003600-210028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:210003800-210028000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:210003800-210028200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:210003800-210028400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:210004000-210019000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:210004000-210019000	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:210004000-210021400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:210004000-210027600	Strong transcription	K562	blood
18	chr1:210004000-210027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:210004000-210028000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:210004000-210028000	Strong transcription	Fetal Thymus	thymus
21	chr1:210004000-210028200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr1:210004000-210030800	Strong transcription	Primary B cells from cord blood	blood
23	chr1:210004200-210018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:210004200-210018800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:210004200-210019000	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr1:210004200-210019000	Strong transcription	Brain Anterior Caudate	brain
27	chr1:210004200-210019400	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:210004200-210019400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr1:210004200-210020200	Strong transcription	Brain Angular Gyrus	brain
30	chr1:210004200-210020200	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:210004200-210022000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr1:210004200-210027600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr1:210004200-210027600	Strong transcription	Primary hematopoietic stem cells	blood
34	chr1:210004200-210027600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr1:210004200-210027800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:210004200-210027800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:210004200-210028000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:210004200-210028400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:210004200-210028400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:210004200-210028800	Strong transcription	Adipose Nuclei	Adipose
41	chr1:210004200-210029600	Strong transcription	Fetal Muscle Leg	muscle
42	chr1:210004200-210030200	Strong transcription	Primary T cells from cord blood	blood
43	chr1:210004400-210019800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:210004400-210019800	Strong transcription	Placenta	Placenta
45	chr1:210004400-210029400	Strong transcription	Dnd41	blood
46	chr1:210004600-210028000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:210004600-210028000	Strong transcription	GM12878-XiMat	blood
48	chr1:210005400-210020000	Strong transcription	Rectal Smooth Muscle	rectum
49	chr1:210006200-210025400	Strong transcription	Brain Hippocampus Middle	brain
50	chr1:210006600-210018800	Strong transcription	Brain Cingulate Gyrus	brain

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