Variant report

Variant	rs6572999
Chromosome Location	chr14:55527374-55527375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:55527363-55527424	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr14:55527347-55527921	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:55527228-55528231	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:55527287-55527885	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr14:55527260-55528162	A549	lung:	n/a	n/a
6	POLR2A	chr14:55527318-55527542	GM12891	blood:	n/a	n/a
7	POLR2A	chr14:55527350-55527749	K562	blood:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55524853..55528129-chr14:55532320..55535008,3	MCF-7	breast:
2	chr14:55526794..55528357-chr14:55606390..55608686,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SOCS4-1	chr14:55527080-55527500	NONHSAT036983

No data

Variant related genes	Relation type
MAPK1IP1L	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1002054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135721	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10140164	0.81[JPT][hapmap]
rs10145170	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10145268	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10220693	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1107960	0.80[JPT][hapmap]
rs11848846	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11849090	0.86[ASN][1000 genomes]
rs11849878	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11849961	0.89[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs11851178	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs1187876	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1187877	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1187878	0.93[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs1187881	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1187882	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs1187883	0.81[CEU][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs1201378	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]
rs1209087	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]
rs13379159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128120	0.87[JPT][hapmap]
rs17128128	0.90[ASN][1000 genomes]
rs17128132	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs17128145	1.00[CHB][hapmap];0.81[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17832311	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1952085	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147964	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2251366	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2340921	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2878172	0.81[JPT][hapmap]
rs2878174	0.87[JPT][hapmap]
rs3742564	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]
rs4335711	0.81[JPT][hapmap]
rs56262555	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56725788	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805089	0.90[ASN][1000 genomes]
rs6573000	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6573001	0.82[EUR][1000 genomes]
rs7141975	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7144652	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.90[ASN][1000 genomes]
rs7150145	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7151224	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7151431	0.89[ASN][1000 genomes]
rs7153937	0.81[JPT][hapmap]
rs7161656	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs748017	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8004416	0.86[EUR][1000 genomes]
rs8005399	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8008134	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8012152	0.87[JPT][hapmap]
rs8012156	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8012676	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8019390	0.81[JPT][hapmap]
rs8019978	0.85[CEU][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs8020545	0.81[JPT][hapmap]
rs8021929	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8022049	0.87[JPT][hapmap]
rs8022238	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8022405	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9323278	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6572999	FBXO34	cis	cerebellum	SCAN
rs6572999	ATG14	cis	parietal	SCAN
rs6572999	WDHD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55519200-55529400	Weak transcription	Spleen	Spleen
2	chr14:55519400-55529200	Weak transcription	Pancreas	Pancrea
3	chr14:55519600-55528600	Weak transcription	Colonic Mucosa	Colon
4	chr14:55519600-55529400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:55519600-55529400	Weak transcription	Esophagus	oesophagus
6	chr14:55519600-55534400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:55519600-55538000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:55520000-55528600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr14:55520000-55529400	Weak transcription	Aorta	Aorta
10	chr14:55520000-55529400	Weak transcription	Fetal Brain Female	brain
11	chr14:55520200-55528000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr14:55520200-55528400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr14:55520200-55529000	Weak transcription	Brain Anterior Caudate	brain
14	chr14:55520200-55529000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr14:55520200-55529200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr14:55520200-55529600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr14:55520200-55538400	Weak transcription	Fetal Kidney	kidney
18	chr14:55520400-55529000	Weak transcription	Brain Germinal Matrix	brain
19	chr14:55520400-55538200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr14:55520600-55528400	Weak transcription	Colon Smooth Muscle	Colon
21	chr14:55520600-55528600	Weak transcription	Stomach Mucosa	stomach
22	chr14:55520600-55528600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr14:55520600-55529000	Weak transcription	Fetal Lung	lung
24	chr14:55520600-55529000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr14:55520600-55529200	Weak transcription	Brain Substantia Nigra	brain
26	chr14:55520600-55533600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr14:55520600-55535000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr14:55520600-55538000	Weak transcription	Psoas Muscle	Psoas
29	chr14:55520600-55538600	Weak transcription	Fetal Brain Male	brain
30	chr14:55520800-55529400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr14:55520800-55529400	Weak transcription	Brain Angular Gyrus	brain
32	chr14:55520800-55534800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr14:55520800-55535200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr14:55521000-55529600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr14:55521200-55528400	Weak transcription	Liver	Liver
36	chr14:55521200-55529400	Weak transcription	Right Ventricle	heart
37	chr14:55521600-55529400	Weak transcription	Primary B cells from cord blood	blood
38	chr14:55521600-55529400	Weak transcription	HSMMtube	muscle
39	chr14:55521600-55535400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr14:55521600-55535400	Strong transcription	NHEK	skin
41	chr14:55522000-55535600	Strong transcription	Fetal Thymus	thymus
42	chr14:55522400-55529000	Weak transcription	K562	blood
43	chr14:55522400-55529200	Weak transcription	Primary T cells from cord blood	blood
44	chr14:55522600-55528400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr14:55522600-55529600	Weak transcription	Right Atrium	heart
46	chr14:55522600-55532200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr14:55522600-55536600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr14:55523000-55529000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr14:55523200-55528800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr14:55523200-55528800	Weak transcription	Fetal Heart	heart

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