Variant report

Variant	rs4902359
Chromosome Location	chr14:65542790-65542791
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65542410..65545761-chr14:65567808..65570933,3	MCF-7	breast:
2	chr14:65534580..65538429-chr14:65542386..65544897,3	K562	blood:
3	chr14:65540391..65543232-chr14:65544493..65546797,2	K562	blood:
4	chr14:65542480..65545199-chr14:65545922..65548656,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000125952	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10143198	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10151162	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11158574	0.81[CEU][hapmap]
rs1124751	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1124752	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];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11625045	0.83[EUR][1000 genomes]
rs1256417	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1270074	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1271582	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1953228	0.84[EUR][1000 genomes]
rs1953232	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1957948	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1957949	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998688	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2093989	0.92[EUR][1000 genomes]
rs2151755	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2763888	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2781373	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]
rs2781374	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2781375	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34459643	0.80[EUR][1000 genomes]
rs35410051	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35520739	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs45604339	0.87[EUR][1000 genomes]
rs4899161	0.83[CEU][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs4902357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902358	0.85[EUR][1000 genomes]
rs4902360	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	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902362	0.84[ASN][1000 genomes]
rs55658675	0.83[EUR][1000 genomes]
rs7143495	0.81[EUR][1000 genomes]
rs7145112	0.85[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7150646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152277	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7154852	0.84[EUR][1000 genomes]
rs7156617	0.83[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs7158239	0.93[ASW][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7159443	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7161394	0.84[EUR][1000 genomes]
rs762810	0.83[EUR][1000 genomes]
rs8005829	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8008095	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8010213	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8015921	0.93[ASW][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.80[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8181937	0.81[EUR][1000 genomes]
rs8181938	0.81[EUR][1000 genomes]
rs8181939	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs942626	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942627	0.84[EUR][1000 genomes]
rs942628	0.93[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942629	0.86[ASW][hapmap];0.81[CEU][hapmap];0.85[CHB][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs998247	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[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
rs4902359	RAB15	cis	cerebellum	SCAN
rs4902359	WDR89	cis	cerebellum	SCAN
rs4902359	MAX	cis	parietal	SCAN
rs4902359	GPX2	cis	cerebellum	SCAN
rs4902359	MAX	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65471200-65546200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr14:65501800-65543200	Weak transcription	Fetal Brain Male	brain
3	chr14:65527600-65545600	Strong transcription	Primary T cells from cord blood	blood
4	chr14:65527800-65553600	Strong transcription	Dnd41	blood
5	chr14:65528800-65555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr14:65529800-65543000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr14:65530000-65553000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:65530400-65543200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr14:65534000-65553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:65534600-65546000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr14:65534800-65553400	Strong transcription	Thymus	Thymus
12	chr14:65535600-65545600	Strong transcription	Fetal Stomach	stomach
13	chr14:65535600-65547000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr14:65536000-65553600	Strong transcription	Fetal Thymus	thymus
15	chr14:65536600-65543200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:65536800-65542800	Weak transcription	Fetal Lung	lung
17	chr14:65537600-65542800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr14:65537600-65543200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr14:65538200-65544600	Strong transcription	HSMM	muscle
20	chr14:65538400-65545000	Strong transcription	GM12878-XiMat	blood
21	chr14:65538400-65545600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr14:65538600-65547000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:65538600-65547000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr14:65538800-65545600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr14:65538800-65553600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr14:65538800-65562000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr14:65539000-65544800	Strong transcription	Fetal Brain Female	brain
28	chr14:65539000-65551000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr14:65539000-65562400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:65539200-65543800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr14:65539200-65545400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:65539200-65548800	Strong transcription	NHEK	skin
33	chr14:65539200-65550800	Strong transcription	Fetal Muscle Trunk	muscle
34	chr14:65539200-65551400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr14:65539400-65545000	Strong transcription	NHLF	lung
36	chr14:65539400-65551000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:65539400-65552400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr14:65539600-65543400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr14:65539600-65547200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr14:65539600-65547400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr14:65539600-65563200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr14:65539800-65544800	Genic enhancers	Left Ventricle	heart
43	chr14:65539800-65547200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr14:65539800-65547400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:65539800-65553200	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr14:65540000-65546000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr14:65540200-65544800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr14:65540400-65543400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr14:65540400-65543600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr14:65540400-65543800	Genic enhancers	Lung	lung

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