Variant report

Variant	rs6772028
Chromosome Location	chr3:178785549-178785550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178763837..178765875-chr3:178785002..178787931,2	K562	blood:
2	chr3:178784601..178786861-chr3:178787060..178790095,4	MCF-7	breast:
3	chr3:178778004..178779935-chr3:178784372..178786776,2	MCF-7	breast:
4	chr3:178785014..178787957-chr3:178798169..178800614,2	K562	blood:

Variant related genes	Relation type
ENSG00000172667	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11711320	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11720081	0.81[EUR][1000 genomes]
rs1542	0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2677770	0.93[GIH][hapmap]
rs2699887	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs2699905	0.80[CEU][hapmap];0.93[GIH][hapmap]
rs4245914	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4279147	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4280676	0.81[EUR][1000 genomes]
rs4315724	0.81[EUR][1000 genomes]
rs4337680	0.81[EUR][1000 genomes]
rs4377525	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4395442	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4417911	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425305	0.88[ASN][1000 genomes]
rs4469018	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4501160	0.81[EUR][1000 genomes]
rs4505756	0.81[EUR][1000 genomes]
rs4552405	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4579062	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607155	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4626139	0.81[EUR][1000 genomes]
rs4632588	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637331	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955796	0.81[EUR][1000 genomes]
rs4955807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4955810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56115013	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443614	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443617	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6443618	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6784495	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6790867	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793769	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793893	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6794165	0.87[AMR][1000 genomes]
rs6794956	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795238	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800015	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7429173	0.81[EUR][1000 genomes]
rs7612363	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7633318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7639391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651510	0.81[EUR][1000 genomes]
rs7652946	0.81[EUR][1000 genomes]
rs9830482	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9831543	0.84[CEU][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs9835752	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835765	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846511	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9860318	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9860749	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9878734	0.97[ASN][1000 genomes]
rs9879637	0.81[EUR][1000 genomes]
rs9880749	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9968179	0.85[CEU][hapmap];0.93[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv461026	chr3:178661814-178886609	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv592649	chr3:178661814-178886609	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv1792927	chr3:178734558-178877169	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv1841799	chr3:178739594-178884337	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6772028	YEATS2	cis	cerebellum	SCAN
rs6772028	ATP11B	cis	parietal	SCAN
rs6772028	KCNMB3	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178755600-178787800	Weak transcription	Aorta	Aorta
2	chr3:178756800-178788400	Weak transcription	Fetal Intestine Small	intestine
3	chr3:178756800-178788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:178764200-178787000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:178764800-178787200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:178764800-178789000	Weak transcription	Lung	lung
7	chr3:178765000-178786800	Weak transcription	Dnd41	blood
8	chr3:178765200-178789000	Weak transcription	Spleen	Spleen
9	chr3:178768400-178788800	Weak transcription	Small Intestine	intestine
10	chr3:178768600-178788800	Weak transcription	Placenta	Placenta
11	chr3:178771000-178788400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:178772000-178786800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:178772600-178788800	Weak transcription	Esophagus	oesophagus
14	chr3:178773600-178788600	Weak transcription	Fetal Stomach	stomach
15	chr3:178775000-178786000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:178777800-178788400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:178778200-178788600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:178778400-178785600	Strong transcription	Osteobl	bone
19	chr3:178779000-178785600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:178779200-178787800	Weak transcription	Fetal Brain Male	brain
21	chr3:178779800-178787200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:178780000-178785600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr3:178780000-178786000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:178780200-178785600	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr3:178780200-178788800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:178780400-178787600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:178780600-178785800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:178780800-178786800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:178781000-178786600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:178781000-178786800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:178781000-178787200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:178781400-178786000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr3:178781600-178785600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:178781600-178786000	Strong transcription	Fetal Thymus	thymus
35	chr3:178781800-178788400	Weak transcription	Right Atrium	heart
36	chr3:178782200-178785600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr3:178782400-178785600	Weak transcription	Stomach Mucosa	stomach
38	chr3:178782400-178788400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:178782600-178785600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:178782600-178785800	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:178782600-178786000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:178782600-178786600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:178782600-178787800	Weak transcription	Colon Smooth Muscle	Colon
44	chr3:178782600-178788800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr3:178782600-178788800	Weak transcription	Psoas Muscle	Psoas
46	chr3:178782800-178785600	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr3:178783200-178785600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
48	chr3:178783400-178788400	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:178783400-178788600	Weak transcription	Right Ventricle	heart
50	chr3:178783600-178785800	Strong transcription	Duodenum Mucosa	Duodenum

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