Variant report

Variant	rs3778017
Chromosome Location	chr6:36842183-36842184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36807524..36809361-chr6:36841077..36843091,2	K562	blood:
2	chr22:24255806..24256650-chr6:36842066..36842781,2	Hela-S3	cervix:
3	chr6:36842114..36842903-chr9:130213220..130213862,2	Hela-S3	cervix:
4	chr6:36840111..36842444-chr6:37018601..37020201,2	MCF-7	breast:
5	chr6:36839698..36842485-chr6:36952323..36954016,2	K562	blood:
6	chr6:36841771..36843991-chr6:36852556..36855136,3	MCF-7	breast:
7	chr6:36841338..36845965-chr6:36851992..36855231,4	MCF-7	breast:
8	chr6:36838369..36843263-chr6:36951921..36955568,5	MCF-7	breast:
9	chr6:36561980..36564185-chr6:36840792..36844090,3	K562	blood:
10	chr6:36735629..36738074-chr6:36841042..36842717,2	K562	blood:
11	chr6:36807086..36809328-chr6:36841078..36843476,3	K562	blood:
12	chr6:36562065..36563624-chr6:36841124..36842701,2	K562	blood:
13	chr6:36841093..36843369-chr6:37223969..37226953,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000172738	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000197958	Chromatin interaction
ENSG00000198663	Chromatin interaction
ENSG00000148356	Chromatin interaction
ENSG00000065491	Chromatin interaction
ENSG00000124772	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1150784	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12528273	0.81[JPT][hapmap]
rs2116447	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293393	0.84[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2303993	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236349	0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs236352	0.96[ASN][1000 genomes]
rs236385	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs236386	0.80[CHB][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap]
rs3756905	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3778016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846871	0.95[ASN][1000 genomes]
rs449840	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4594944	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs460539	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4714018	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.95[ASN][1000 genomes]
rs58214515	0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs62406643	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6457963	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6909988	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6910832	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6914008	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6934844	0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7743646	0.83[LWK][hapmap]
rs831480	0.80[CHB][hapmap]
rs8472	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366920	0.98[ASN][1000 genomes]
rs9368966	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380610	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs9380616	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9380618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380626	0.86[ASN][1000 genomes]
rs9470426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3778017	PPIL1	Cis_1M	lymphoblastoid	RTeQTL
rs3778017	LRFN2	cis	cerebellum	SCAN
rs3778017	GLP1R	cis	parietal	SCAN
rs3778017	PNPLA1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36837000-36842200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:36840400-36842200	Enhancers	Spleen	Spleen
3	chr6:36841000-36843200	Active TSS	GM12878-XiMat	blood
4	chr6:36841200-36842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:36841200-36843200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:36841400-36842200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:36841400-36842200	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr6:36841400-36842200	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr6:36841400-36842200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr6:36841400-36842200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
11	chr6:36841400-36842200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
12	chr6:36841400-36842200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr6:36841400-36842200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:36841400-36842200	Flanking Active TSS	Liver	Liver
15	chr6:36841400-36842200	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr6:36841400-36842200	Flanking Active TSS	Brain Hippocampus Middle	brain
17	chr6:36841400-36842200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr6:36841400-36842200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr6:36841400-36842400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr6:36841400-36842400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr6:36841400-36843200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:36841400-36843200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:36841400-36843400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:36841400-36843400	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:36841400-36843400	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:36841600-36842200	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr6:36841600-36842200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr6:36841600-36842200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr6:36841600-36842200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr6:36841600-36842200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr6:36841600-36842200	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr6:36841600-36843200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:36841600-36843200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:36841600-36843200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:36841600-36843200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:36841600-36843200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:36841600-36843200	Active TSS	Psoas Muscle	Psoas
38	chr6:36841600-36843200	Active TSS	Small Intestine	intestine
39	chr6:36841600-36843400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr6:36841600-36843400	Active TSS	Right Atrium	heart
41	chr6:36841600-36843400	Active TSS	A549	lung
42	chr6:36841600-36843800	Active TSS	Fetal Muscle Trunk	muscle
43	chr6:36841800-36842200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr6:36841800-36842200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:36841800-36842200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr6:36841800-36842200	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr6:36841800-36842400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr6:36841800-36842800	Active TSS	Gastric	stomach
49	chr6:36841800-36843000	Active TSS	Esophagus	oesophagus
50	chr6:36841800-36843000	Active TSS	Fetal Brain Male	brain

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