Variant report

Variant	rs3742564
Chromosome Location	chr14:55530120-55530121
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	chr14:54907732..54909904-chr14:55529224..55531676,2	K562	blood:

Variant related genes	Relation type
ENSG00000100528	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1002054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10135721	0.84[ASN][1000 genomes]
rs10140164	0.81[JPT][hapmap]
rs10145170	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10145268	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10220693	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1107960	0.80[JPT][hapmap]
rs11849090	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11849878	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11851178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1187876	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1187877	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.94[ASN][1000 genomes]
rs1187878	0.96[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1187881	0.84[ASN][1000 genomes]
rs1187882	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1187883	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs1201378	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1209087	0.92[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13379159	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17128120	0.87[JPT][hapmap]
rs17128128	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128132	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17128145	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17832311	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1952085	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2251366	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2878172	0.81[JPT][hapmap]
rs2878174	0.87[JPT][hapmap]
rs4335711	0.81[JPT][hapmap]
rs56262555	0.81[ASN][1000 genomes]
rs56725788	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60805089	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6572999	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573000	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7141975	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7144652	0.92[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7146285	0.87[JPT][hapmap]
rs7149965	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7150145	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7151224	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7151431	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7153937	0.81[JPT][hapmap]
rs7161656	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs748017	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8005399	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8008134	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8012152	0.87[JPT][hapmap]
rs8012156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8019390	0.81[JPT][hapmap]
rs8020545	0.81[JPT][hapmap]
rs8021929	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8022049	0.87[JPT][hapmap]
rs8022238	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8022405	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9323278	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9806049	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv977468	chr14:55529336-55531777	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3742564	ATG14	cis	parietal	SCAN
rs3742564	RPL13AP3	cis	cerebellum	SCAN
rs3742564	FBXO34	cis	cerebellum	SCAN
rs3742564	WDHD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55519600-55534400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:55519600-55538000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr14:55520200-55538400	Weak transcription	Fetal Kidney	kidney
4	chr14:55520400-55538200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:55520600-55533600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr14:55520600-55535000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:55520600-55538000	Weak transcription	Psoas Muscle	Psoas
8	chr14:55520600-55538600	Weak transcription	Fetal Brain Male	brain
9	chr14:55520800-55534800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr14:55520800-55535200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:55521600-55535400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr14:55521600-55535400	Strong transcription	NHEK	skin
13	chr14:55522000-55535600	Strong transcription	Fetal Thymus	thymus
14	chr14:55522600-55532200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr14:55522600-55536600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr14:55523200-55533200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr14:55523600-55533600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr14:55523600-55535200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr14:55524200-55535400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr14:55524400-55533400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr14:55524400-55536600	Strong transcription	Osteobl	bone
22	chr14:55524600-55533600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr14:55524600-55533600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr14:55524600-55534800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr14:55524800-55531800	Strong transcription	HMEC	breast
26	chr14:55524800-55535600	Strong transcription	A549	lung
27	chr14:55524800-55535800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr14:55526000-55534800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr14:55526200-55536000	Strong transcription	Primary hematopoietic stem cells	blood
30	chr14:55526400-55538000	Weak transcription	Small Intestine	intestine
31	chr14:55526600-55531000	Strong transcription	Fetal Intestine Small	intestine
32	chr14:55526600-55535800	Strong transcription	Dnd41	blood
33	chr14:55526600-55537600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:55526600-55538400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr14:55527200-55532800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr14:55527200-55533600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr14:55527400-55530400	Strong transcription	Fetal Stomach	stomach
38	chr14:55527400-55530800	Strong transcription	Primary B cells from peripheral blood	blood
39	chr14:55527400-55531000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:55527400-55531000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr14:55527400-55532600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr14:55527400-55533400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr14:55527400-55535200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr14:55527600-55531400	Strong transcription	Fetal Intestine Large	intestine
45	chr14:55527600-55533600	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:55527600-55534800	Strong transcription	HUVEC	blood vessel
47	chr14:55527800-55533600	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr14:55528000-55532000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr14:55528000-55532600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr14:55528000-55534600	Strong transcription	NH-A	brain

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