Variant report

Variant	rs3778111
Chromosome Location	chr6:119668299-119668300
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:119646382..119648660-chr6:119668105..119670795,4	K562	blood:
2	chr6:119606943..119609052-chr6:119667352..119668942,2	K562	blood:
3	chr6:119666964..119669354-chr6:119827597..119829582,2	K562	blood:
4	chr6:119460572..119463135-chr6:119668179..119670876,2	K562	blood:
5	chr6:119658599..119660724-chr6:119666324..119670101,4	K562	blood:

Variant related genes	Relation type
ENSG00000200732	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12209570	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap]
rs1295386	0.86[MKK][hapmap];0.82[YRI][hapmap]
rs1295391	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1295392	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs195048	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs195056	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs195058	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs195090	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs195092	0.81[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2057554	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2299878	0.89[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs2299886	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2357164	0.89[CEU][hapmap];0.90[YRI][hapmap];0.84[EUR][1000 genomes]
rs3819731	0.81[EUR][1000 genomes]
rs4946406	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6569074	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6937640	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7755155	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7755572	0.86[EUR][1000 genomes]
rs7757317	0.88[LWK][hapmap]
rs9374788	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9489638	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs975578	0.84[EUR][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	nsv1025995	chr6:119407742-119709548	Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv1802628	chr6:119647135-119678881	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3778111	ASF1A	cis	cerebellum	SCAN
rs3778111	GPRC6A	cis	cerebellum	SCAN
rs3778111	FAM184A	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119625200-119668600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:119662200-119669200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:119662600-119668600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:119664400-119668600	Transcr. at gene 5' and 3'	K562	blood
5	chr6:119664800-119672400	Active TSS	Brain Anterior Caudate	brain
6	chr6:119665000-119668600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr6:119665000-119669200	Weak transcription	Spleen	Spleen
8	chr6:119665200-119672800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr6:119665600-119668600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:119666200-119672600	Active TSS	NHDF-Ad	bronchial
11	chr6:119666600-119668600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr6:119666600-119672400	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr6:119666800-119669000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:119666800-119669000	Flanking Active TSS	GM12878-XiMat	blood
15	chr6:119667000-119669400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:119667000-119672400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:119667000-119672400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:119667000-119672800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:119667200-119668400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:119667200-119669200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:119667200-119672200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr6:119667200-119672400	Active TSS	Right Atrium	heart
23	chr6:119667400-119668400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:119667400-119668400	Active TSS	Fetal Stomach	stomach
25	chr6:119667400-119668600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr6:119667400-119668800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr6:119667400-119669000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr6:119667400-119670400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:119667400-119670400	Active TSS	Placenta	Placenta
30	chr6:119667400-119670600	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr6:119667600-119668400	Enhancers	H9 Cell Line	embryonic stem cell
32	chr6:119667600-119668400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr6:119667600-119668400	Flanking Active TSS	Fetal Heart	heart
34	chr6:119667600-119668400	Flanking Active TSS	Dnd41	blood
35	chr6:119667600-119668600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:119667600-119668600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
37	chr6:119667600-119668800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:119667600-119668800	Enhancers	NH-A	brain
39	chr6:119667600-119669200	Active TSS	Brain Cingulate Gyrus	brain
40	chr6:119667600-119669200	Enhancers	HUVEC	blood vessel
41	chr6:119667600-119669400	Active TSS	Colonic Mucosa	Colon
42	chr6:119667600-119669600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr6:119667600-119669600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
44	chr6:119667600-119669800	Flanking Active TSS	NHEK	skin
45	chr6:119667600-119670000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr6:119667600-119670200	Active TSS	Fetal Brain Male	brain
47	chr6:119667600-119670400	Active TSS	Brain Hippocampus Middle	brain
48	chr6:119667600-119672000	Active TSS	Lung	lung
49	chr6:119667600-119672000	Active TSS	Pancreas	Pancrea
50	chr6:119667600-119672200	Active TSS	Brain Angular Gyrus	brain

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