Variant report

Variant	rs4902360
Chromosome Location	chr14:65546722-65546723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:65546651-65546997	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:65542480..65545199-chr14:65545922..65548656,2	MCF-7	breast:
2	chr14:65540391..65543232-chr14:65544493..65546797,2	K562	blood:
3	chr14:65536598..65540126-chr14:65544399..65547466,3	MCF-7	breast:
4	chr14:65544997..65548177-chr14:65565453..65571553,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259118	TF binding region
ENSG00000125952	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10143198	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10151162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11158574	0.86[CEU][hapmap]
rs1124751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1124752	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];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11625045	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1256417	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1270074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1271582	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12880781	0.84[CEU][hapmap]
rs1953228	0.82[EUR][1000 genomes]
rs1953232	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1957948	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1957949	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2093989	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2151755	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2763888	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781373	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]
rs2781374	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781375	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35410051	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35520739	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs45604339	0.81[EUR][1000 genomes]
rs4899161	0.92[CEU][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs4902357	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902358	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4902359	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902361	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902362	0.85[ASN][1000 genomes]
rs55658675	0.81[EUR][1000 genomes]
rs7143495	0.84[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs7145112	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7146939	0.81[ASN][1000 genomes]
rs7150646	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7152277	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7154852	0.82[EUR][1000 genomes]
rs7156617	0.92[CEU][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs7158239	0.93[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7159443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161394	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs762810	0.85[EUR][1000 genomes]
rs8005829	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8008095	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8010213	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8015921	0.93[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8181937	0.85[EUR][1000 genomes]
rs8181938	0.85[EUR][1000 genomes]
rs8181939	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs884683	0.82[CEU][hapmap]
rs942626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942627	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs942628	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942629	0.86[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998247	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[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
rs4902360	GPX2	cis	cerebellum	SCAN
rs4902360	WDR89	cis	cerebellum	SCAN
rs4902360	RAB15	cis	cerebellum	SCAN
rs4902360	MAX	cis	cerebellum	SCAN
rs4902360	MAX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65527800-65553600	Strong transcription	Dnd41	blood
2	chr14:65528800-65555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:65530000-65553000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:65534000-65553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr14:65534800-65553400	Strong transcription	Thymus	Thymus
6	chr14:65535600-65547000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr14:65536000-65553600	Strong transcription	Fetal Thymus	thymus
8	chr14:65538600-65547000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:65538600-65547000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr14:65538800-65553600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr14:65538800-65562000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr14:65539000-65551000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr14:65539000-65562400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr14:65539200-65548800	Strong transcription	NHEK	skin
15	chr14:65539200-65550800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr14:65539200-65551400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:65539400-65551000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr14:65539400-65552400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:65539600-65547200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:65539600-65547400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr14:65539600-65563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr14:65539800-65547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr14:65539800-65547400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr14:65539800-65553200	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr14:65540400-65548000	Strong transcription	Osteobl	bone
26	chr14:65541000-65551600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr14:65541600-65551000	Strong transcription	NH-A	brain
28	chr14:65541600-65552400	Strong transcription	Hela-S3	cervix
29	chr14:65541800-65549800	Strong transcription	HepG2	liver
30	chr14:65542000-65547400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr14:65542000-65548800	Strong transcription	A549	lung
32	chr14:65542200-65547200	Strong transcription	Liver	Liver
33	chr14:65542200-65547400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr14:65542200-65547600	Strong transcription	Primary B cells from peripheral blood	blood
35	chr14:65542200-65548000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr14:65542200-65548800	Strong transcription	HMEC	breast
37	chr14:65542400-65550400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr14:65542800-65550800	Strong transcription	Fetal Lung	lung
39	chr14:65543000-65547400	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr14:65543000-65550800	Strong transcription	HSMMtube	muscle
41	chr14:65543400-65549200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr14:65543800-65548000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr14:65543800-65551000	Genic enhancers	Fetal Intestine Large	intestine
44	chr14:65544000-65552400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr14:65544400-65553600	Weak transcription	Fetal Brain Male	brain
46	chr14:65544600-65548400	Weak transcription	NHDF-Ad	bronchial
47	chr14:65544600-65551400	Genic enhancers	Fetal Intestine Small	intestine
48	chr14:65544600-65553600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr14:65544800-65546800	Weak transcription	Fetal Brain Female	brain
50	chr14:65544800-65547200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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