Variant report

Variant	rs1209087
Chromosome Location	chr14:55493220-55493221
allele	A/G
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	chr14:55493060-55494651	Hela-S3	cervix:	n/a	n/a
2	JUN	chr14:55492821-55494263	K562	blood:	n/a	chr14:55493336-55493343 chr14:55493334-55493345 chr14:55493338-55493347 chr14:55493338-55493346 chr14:55493339-55493346
3	FOS	chr14:55493164-55493532	MCF10A-Er-Src	breast:	n/a	chr14:55493336-55493343 chr14:55493334-55493345 chr14:55493338-55493347 chr14:55493338-55493346 chr14:55493339-55493346
4	MAFF	chr14:55493198-55493520	HepG2	liver:	n/a	n/a
5	MAFK	chr14:55493172-55493547	IMR90	lung:	n/a	n/a
6	NRF1	chr14:55493173-55493347	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr14:55493164-55493449	MCF10A-Er-Src	breast:	n/a	chr14:55493337-55493346 chr14:55493338-55493347
8	MXI1	chr14:55492547-55495304	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr14:55493186-55494212	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr14:55493185-55493959	HepG2	liver:	n/a	n/a
11	POLR2A	chr14:55493172-55494496	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr14:55493194-55494579	IMR90	lung:	n/a	n/a
13	E2F4	chr14:55493068-55494109	MCF10A-Er-Src	breast:	n/a	chr14:55493786-55493797 chr14:55493818-55493827
14	SIN3A	chr14:55492237-55494788	H1-hESC	embryonic stem cell:	n/a	n/a
15	TAF1	chr14:55493199-55494531	ECC-1	luminal epithelium:	n/a	n/a
16	CEBPB	chr14:55493166-55494312	Hela-S3	cervix:	n/a	n/a
17	SIN3AK20	chr14:55493204-55494542	MCF-7	breast:	n/a	n/a
18	MAFK	chr14:55493157-55494234	Hela-S3	cervix:	n/a	n/a
19	MYC	chr14:55493032-55494404	A549	lung:	n/a	chr14:55493833-55493842 chr14:55493337-55493346 chr14:55493338-55493347
20	HCFC1	chr14:55492961-55494577	Hela-S3	cervix:	n/a	n/a
21	TBP	chr14:55493217-55494630	Hela-S3	cervix:	n/a	n/a
22	EP300	chr14:55492986-55493225	GM12878	blood:	n/a	n/a
23	POLR2A	chr14:55493048-55494462	H1-hESC	embryonic stem cell:	n/a	n/a
24	TAF7	chr14:55493096-55494484	H1-hESC	embryonic stem cell:	n/a	n/a
25	CHD1	chr14:55493218-55494846	GM12878	blood:	n/a	n/a
26	CHD1	chr14:55492126-55494811	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr14:55491898-55494569	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAFK	chr14:55493194-55493527	HepG2	liver:	n/a	n/a
29	SIX5	chr14:55493164-55494214	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55490790..55495805-chr14:55515486..55522658,19	MCF-7	breast:
2	chr1:17231023..17232250-chr14:55493199..55494239,3	Hela-S3	cervix:
3	chr14:55491083..55496744-chr14:55514437..55523536,23	MCF-7	breast:
4	chr14:55492412..55494140-chr14:55594962..55596941,2	MCF-7	breast:
5	chr14:55491921..55500295-chr14:55515389..55520812,24	K562	blood:
6	chr14:55491992..55498342-chr14:55515529..55520367,21	K562	blood:

Variant related genes	Relation type
SOCS4	TF binding region
ENSG00000168175	Chromatin interaction
ENSG00000272426	Chromatin interaction
ENSG00000131981	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1002054	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10135721	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10140164	0.81[JPT][hapmap]
rs10145170	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10145268	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10220693	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1107960	0.80[JPT][hapmap]
rs11849090	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11849878	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11849961	0.93[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11851178	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1187876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1187877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1187878	0.93[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1187881	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1187882	0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1187883	0.85[CEU][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1201378	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13379159	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17128120	0.87[JPT][hapmap]
rs17128128	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17128132	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17128145	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs17832311	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1952085	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2147964	0.81[CEU][hapmap]
rs2251366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2340921	0.81[CEU][hapmap]
rs2878172	0.81[JPT][hapmap]
rs2878174	0.87[JPT][hapmap]
rs3742564	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]
rs4335711	0.81[JPT][hapmap]
rs56725788	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60805089	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6572999	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6573000	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7141975	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7144652	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7146285	0.87[JPT][hapmap]
rs7149965	1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7150145	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7151224	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7151431	0.87[ASN][1000 genomes]
rs7153937	0.81[JPT][hapmap]
rs7161656	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs748017	0.90[EUR][1000 genomes]
rs8005399	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8008134	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8012152	0.87[JPT][hapmap]
rs8012156	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs8019390	0.81[JPT][hapmap]
rs8019978	0.81[CEU][hapmap];0.93[TSI][hapmap]
rs8020545	0.81[JPT][hapmap]
rs8021929	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8022049	0.87[JPT][hapmap]
rs8022238	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8022405	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9323278	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9806049	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.86[MKK][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.91[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1209087	FBXO34	cis	cerebellum	SCAN
rs1209087	WDHD1	cis	parietal	SCAN
rs1209087	MUDENG	cis	parietal	SCAN
rs1209087	ATG14	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55472000-55493400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:55473000-55493400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:55486400-55493400	Weak transcription	Left Ventricle	heart
4	chr14:55491200-55493400	Weak transcription	Gastric	stomach
5	chr14:55491200-55495800	Active TSS	H1 Cell Line	embryonic stem cell
6	chr14:55491400-55495200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr14:55491400-55495200	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr14:55492000-55496200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:55492000-55496400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr14:55492200-55493400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr14:55492200-55493400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr14:55492200-55493400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr14:55492200-55493600	Flanking Active TSS	HUVEC	blood vessel
14	chr14:55492200-55495200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr14:55492200-55495200	Active TSS	Brain Germinal Matrix	brain
16	chr14:55492200-55496000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr14:55492400-55493400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr14:55492400-55493400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr14:55492400-55493400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr14:55492400-55493600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr14:55492400-55494800	Active TSS	Fetal Thymus	thymus
22	chr14:55492400-55495200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr14:55492400-55495200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr14:55492400-55495600	Active TSS	Fetal Kidney	kidney
25	chr14:55492400-55496800	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr14:55492600-55493400	Flanking Active TSS	Osteobl	bone
27	chr14:55492600-55493800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:55492600-55495000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr14:55492600-55495200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:55492600-55495200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr14:55492600-55495200	Active TSS	Fetal Muscle Trunk	muscle
32	chr14:55492600-55495400	Active TSS	H9 Cell Line	embryonic stem cell
33	chr14:55492600-55495400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
34	chr14:55492600-55495800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr14:55492800-55493400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr14:55492800-55493400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr14:55492800-55493400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr14:55492800-55493400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr14:55492800-55493400	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr14:55492800-55493400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr14:55492800-55493600	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr14:55492800-55493600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr14:55492800-55493600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr14:55492800-55493600	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr14:55492800-55493600	Flanking Active TSS	Rectal Smooth Muscle	rectum
46	chr14:55492800-55493800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr14:55492800-55494400	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr14:55492800-55494800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr14:55492800-55494800	Active TSS	Thymus	Thymus
50	chr14:55492800-55495000	Active TSS	Placenta Amnion	Placenta Amnion

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