Variant report

Variant	rs6800015
Chromosome Location	chr3:178779546-178779547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:178778004..178779935-chr3:178784372..178786776,2	MCF-7	breast:
2	chr3:178770602..178773150-chr3:178777217..178780693,3	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11711320	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1542	0.82[JPT][hapmap]
rs2677770	0.93[GIH][hapmap]
rs2699887	0.93[GIH][hapmap]
rs2699905	0.93[GIH][hapmap]
rs4245914	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4279147	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4377525	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4395442	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4417911	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4425305	0.81[ASN][1000 genomes]
rs4469018	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4552405	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4579062	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4607155	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4632588	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4637331	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955807	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4955810	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56115013	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6443614	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6443617	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6443618	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6772028	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]
rs6784495	0.93[GIH][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6790867	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6793769	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6793893	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6794165	0.84[AMR][1000 genomes]
rs6794956	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6795238	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6804084	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7612363	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7633318	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs7639391	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9830482	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9831543	0.82[JPT][hapmap]
rs9835752	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9835765	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9846511	0.82[AMR][1000 genomes]
rs9860318	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9860749	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9878734	0.89[ASN][1000 genomes]
rs9880749	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9968179	0.93[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1009143	chr3:178731525-178783915	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv1799481	chr3:178733212-178782021	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	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
8	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
rs6800015	YEATS2	cis	cerebellum	SCAN
rs6800015	ATP11B	cis	parietal	SCAN
rs6800015	KCNMB3	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178746000-178784000	Weak transcription	Liver	Liver
2	chr3:178746000-178785200	Weak transcription	Thymus	Thymus
3	chr3:178753600-178784800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:178755600-178787800	Weak transcription	Aorta	Aorta
5	chr3:178756000-178780400	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:178756000-178783600	Weak transcription	NHDF-Ad	bronchial
7	chr3:178756600-178781600	Weak transcription	HMEC	breast
8	chr3:178756600-178781800	Weak transcription	NHLF	lung
9	chr3:178756600-178783800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:178756800-178788400	Weak transcription	Fetal Intestine Small	intestine
11	chr3:178756800-178788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:178757200-178782200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:178764200-178781800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:178764200-178787000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:178764400-178780400	Weak transcription	HepG2	liver
16	chr3:178764400-178784600	Weak transcription	K562	blood
17	chr3:178764600-178780600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:178764600-178782400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:178764800-178785200	Weak transcription	Pancreas	Pancrea
20	chr3:178764800-178787200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:178764800-178789000	Weak transcription	Lung	lung
22	chr3:178765000-178779800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr3:178765000-178785400	Weak transcription	Gastric	stomach
24	chr3:178765000-178786800	Weak transcription	Dnd41	blood
25	chr3:178765200-178780200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:178765200-178781600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:178765200-178781600	Weak transcription	HSMMtube	muscle
28	chr3:178765200-178784600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:178765200-178789000	Weak transcription	Spleen	Spleen
30	chr3:178766800-178779600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:178768400-178784000	Weak transcription	HUVEC	blood vessel
32	chr3:178768400-178788800	Weak transcription	Small Intestine	intestine
33	chr3:178768600-178780600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:178768600-178788800	Weak transcription	Placenta	Placenta
35	chr3:178769200-178784000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:178769400-178780000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:178769600-178782200	Weak transcription	Primary B cells from cord blood	blood
38	chr3:178769800-178783800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr3:178770000-178783800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:178770200-178784800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:178770400-178780200	Weak transcription	Brain Anterior Caudate	brain
42	chr3:178770600-178784800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:178770800-178783800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:178771000-178788400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:178771600-178784800	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:178772000-178786800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:178772600-178780600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:178772600-178782600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr3:178772600-178788800	Weak transcription	Esophagus	oesophagus
50	chr3:178772800-178781800	Weak transcription	Left Ventricle	heart

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