Variant report

Variant	rs942628
Chromosome Location	chr14:65539463-65539464
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65536598..65540126-chr14:65544399..65547466,3	MCF-7	breast:
2	chr14:65539049..65542312-chr14:65547524..65550100,3	K562	blood:
3	chr14:65530728..65534685-chr14:65538811..65541539,3	K562	blood:

Variant related genes	Relation type
ENSG00000259118	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

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

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];0.89[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];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11158574	0.86[CEU][hapmap]
rs1124751	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1124752	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];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11625045	0.84[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs11626720	0.82[EUR][1000 genomes]
rs1256417	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[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];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1271582	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12880781	0.84[CEU][hapmap]
rs1953228	0.85[EUR][1000 genomes]
rs1953232	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1957948	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1998688	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2093989	0.92[EUR][1000 genomes]
rs2151755	0.88[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2763888	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781373	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]
rs2781374	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2781375	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34459643	0.82[EUR][1000 genomes]
rs35410051	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35520739	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs45604339	0.84[EUR][1000 genomes]
rs4899161	0.92[CEU][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes]
rs4902357	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902358	0.84[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs4902359	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]
rs4902360	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]
rs4902361	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902362	0.85[ASN][1000 genomes]
rs55658675	0.84[EUR][1000 genomes]
rs7143495	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7145112	0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7152277	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7154852	0.85[EUR][1000 genomes]
rs7156617	0.92[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs7158239	1.00[ASW][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7159443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7161394	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs762810	0.80[EUR][1000 genomes]
rs8005829	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8008095	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8010213	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8015921	1.00[ASW][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8181937	0.81[EUR][1000 genomes]
rs8181938	0.81[EUR][1000 genomes]
rs8181939	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs884683	0.82[CEU][hapmap]
rs942626	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs942627	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs942629	0.93[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[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];0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs942628	WDR89	cis	cerebellum	SCAN
rs942628	CHURC1	cis	multi-tissue	Pritchard
rs942628	MAX	cis	cerebellum	SCAN
rs942628	MAX	cis	multi-tissue	Pritchard
rs942628	RAB15	cis	cerebellum	SCAN
rs942628	GPX2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65470400-65539600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr14:65471200-65546200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr14:65501800-65543200	Weak transcription	Fetal Brain Male	brain
4	chr14:65508600-65542000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr14:65527400-65539600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr14:65527400-65540400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr14:65527600-65540800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr14:65527600-65545600	Strong transcription	Primary T cells from cord blood	blood
9	chr14:65527800-65553600	Strong transcription	Dnd41	blood
10	chr14:65528800-65555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr14:65529600-65541600	Weak transcription	NH-A	brain
12	chr14:65529800-65543000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:65530000-65553000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:65530400-65543200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr14:65531200-65541400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:65532400-65539600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr14:65532600-65540400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr14:65532600-65542400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr14:65533200-65541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:65533200-65541600	Weak transcription	Hela-S3	cervix
21	chr14:65533200-65542000	Weak transcription	A549	lung
22	chr14:65533400-65542200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr14:65534000-65553600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr14:65534400-65542200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:65534600-65546000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:65534800-65553400	Strong transcription	Thymus	Thymus
27	chr14:65535200-65540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr14:65535400-65539600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr14:65535400-65541600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr14:65535600-65540400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr14:65535600-65545600	Strong transcription	Fetal Stomach	stomach
32	chr14:65535600-65547000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:65536000-65553600	Strong transcription	Fetal Thymus	thymus
34	chr14:65536200-65540800	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr14:65536200-65541800	Enhancers	Fetal Heart	heart
36	chr14:65536200-65541800	Genic enhancers	Fetal Muscle Leg	muscle
37	chr14:65536600-65539600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr14:65536600-65539600	Enhancers	Psoas Muscle	Psoas
39	chr14:65536600-65543200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:65536800-65540000	Weak transcription	HepG2	liver
41	chr14:65536800-65541200	Weak transcription	Aorta	Aorta
42	chr14:65536800-65542800	Weak transcription	Fetal Lung	lung
43	chr14:65537000-65539600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr14:65537000-65540400	Weak transcription	Brain Germinal Matrix	brain
45	chr14:65537000-65541200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr14:65537000-65541600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr14:65537000-65542400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr14:65537400-65539800	Enhancers	NHDF-Ad	bronchial
49	chr14:65537400-65542200	Enhancers	Right Ventricle	heart
50	chr14:65537600-65539600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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