Variant report

Variant	rs2781373
Chromosome Location	chr14:65568215-65568216
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65556086..65557952-chr14:65566751..65569779,3	MCF-7	breast:
2	chr14:65451451..65454703-chr14:65567810..65571977,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257365	Chromatin interaction
ENSG00000259118	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10143198	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10151162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11158572	0.84[EUR][1000 genomes]
rs11158573	0.84[EUR][1000 genomes]
rs11158574	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs1124751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124752	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11625045	0.84[CEU][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs12147959	0.83[EUR][1000 genomes]
rs1256417	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1270074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1271582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12880781	0.84[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs12888794	0.84[EUR][1000 genomes]
rs1953228	0.83[EUR][1000 genomes]
rs1953232	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1957948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1957949	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1998688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2093989	0.91[EUR][1000 genomes]
rs2151755	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2763888	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781375	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34459643	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35410051	0.82[AFR][1000 genomes]
rs35520739	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35769504	0.83[EUR][1000 genomes]
rs45604339	0.81[EUR][1000 genomes]
rs4899161	0.92[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs4902357	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902358	0.84[CEU][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs4902359	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4902360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902361	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902362	0.94[ASN][1000 genomes]
rs55658675	0.83[EUR][1000 genomes]
rs7143495	0.84[CEU][hapmap]
rs7145112	0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7146939	0.89[ASN][1000 genomes]
rs7150646	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7152277	0.84[AFR][1000 genomes]
rs7154852	0.83[EUR][1000 genomes]
rs7156617	0.92[CEU][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs7158239	0.93[ASW][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs7159443	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7161394	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs8005829	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8009396	0.84[EUR][1000 genomes]
rs8009714	0.84[EUR][1000 genomes]
rs8010213	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8015921	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs8181937	0.80[EUR][1000 genomes]
rs8181938	0.80[EUR][1000 genomes]
rs8181939	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs884683	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs942626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs942627	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs942628	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs942629	0.86[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs998247	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2781373	RAB15	cis	cerebellum	SCAN
rs2781373	GPX2	cis	cerebellum	SCAN
rs2781373	WDR89	cis	cerebellum	SCAN
rs2781373	MAX	cis	cerebellum	SCAN
rs2781373	MAX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65556400-65569000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:65560800-65568400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:65561600-65568400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:65562800-65568400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:65563800-65568400	Weak transcription	Pancreas	Pancrea
6	chr14:65563800-65568600	Weak transcription	Spleen	Spleen
7	chr14:65564200-65568400	Weak transcription	Gastric	stomach
8	chr14:65567200-65568400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr14:65567200-65569000	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr14:65567200-65570200	Active TSS	Psoas Muscle	Psoas
11	chr14:65567400-65570000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr14:65567400-65570200	Active TSS	Fetal Intestine Large	intestine
13	chr14:65567600-65568600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr14:65567600-65569400	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr14:65567600-65569800	Active TSS	Primary T cells fromperipheralblood	blood
16	chr14:65567600-65570000	Active TSS	HSMMtube	muscle
17	chr14:65567600-65570200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr14:65567600-65570200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr14:65567600-65570400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr14:65567600-65570600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:65567800-65568400	Flanking Active TSS	Fetal Brain Male	brain
22	chr14:65567800-65568600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr14:65567800-65568600	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr14:65567800-65569800	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr14:65567800-65569800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
26	chr14:65567800-65570000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr14:65567800-65570000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr14:65567800-65570000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr14:65567800-65570000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr14:65567800-65570000	Active TSS	Fetal Thymus	thymus
31	chr14:65567800-65570200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:65567800-65570200	Active TSS	Esophagus	oesophagus
33	chr14:65567800-65570200	Active TSS	Left Ventricle	heart
34	chr14:65567800-65570400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr14:65567800-65570400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:65568000-65568400	Flanking Active TSS	Placenta	Placenta
37	chr14:65568000-65568600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr14:65568000-65569000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr14:65568000-65569200	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr14:65568000-65569600	Active TSS	Duodenum Mucosa	Duodenum
41	chr14:65568000-65569600	Active TSS	Placenta Amnion	Placenta Amnion
42	chr14:65568000-65569600	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr14:65568000-65569600	Active TSS	Stomach Smooth Muscle	stomach
44	chr14:65568000-65569800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr14:65568000-65569800	Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr14:65568000-65569800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr14:65568000-65569800	Active TSS	Lung	lung
48	chr14:65568000-65569800	Active TSS	Dnd41	blood
49	chr14:65568000-65569800	Active TSS	HepG2	liver
50	chr14:65568000-65569800	Active TSS	HMEC	breast

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