Variant report

Variant	rs1201378
Chromosome Location	chr14:55493408-55493409
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	IRF1	chr14:55493397-55494229	K562	blood:	n/a	chr14:55493586-55493595 chr14:55493558-55493568
3	MXI1	chr14:55493314-55494406	Hela-S3	cervix:	n/a	n/a
4	MAX	chr14:55493359-55494485	MCF-7	breast:	n/a	chr14:55493833-55493842
5	SP1	chr14:55493400-55494458	A549	lung:	n/a	chr14:55493829-55493839
6	JUN	chr14:55492821-55494263	K562	blood:	n/a	chr14:55493336-55493343 chr14:55493334-55493345 chr14:55493338-55493347 chr14:55493338-55493346 chr14:55493339-55493346
7	MAX	chr14:55493279-55494456	HCT-116	colon:	n/a	chr14:55493833-55493842 chr14:55493337-55493346 chr14:55493338-55493347
8	MYC	chr14:55493321-55494413	NB4	blood:	n/a	chr14:55493833-55493842 chr14:55493337-55493346 chr14:55493338-55493347
9	POLR2A	chr14:55493370-55494333	HUVEC	blood vessel:	n/a	n/a
10	PML	chr14:55493221-55494572	GM12878	blood:	n/a	chr14:55493339-55493348
11	POLR2A	chr14:55493371-55494406	PANC-1	pancreas:	n/a	n/a
12	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
13	POLR2A	chr14:55493355-55494522	GM12892	blood:	n/a	n/a
14	POLR2A	chr14:55493408-55494397	HL-60	blood:	n/a	n/a
15	MAFF	chr14:55493198-55493520	HepG2	liver:	n/a	n/a
16	MAFK	chr14:55493291-55493495	K562	blood:	n/a	n/a
17	REST	chr14:55493377-55494284	HL-60	blood:	n/a	n/a
18	MAFK	chr14:55493172-55493547	IMR90	lung:	n/a	n/a
19	POLR2A	chr14:55493298-55494493	PBDE	blood:	n/a	n/a
20	MYC	chr14:55493164-55493449	MCF10A-Er-Src	breast:	n/a	chr14:55493337-55493346 chr14:55493338-55493347
21	TAF1	chr14:55493380-55494306	K562	blood:	n/a	n/a
22	MXI1	chr14:55493386-55494301	GM12878	blood:	n/a	n/a
23	ETS1	chr14:55493357-55494221	A549	lung:	n/a	chr14:55493686-55493695 chr14:55494198-55494211 chr14:55493981-55493992
24	FOXM1	chr14:55493378-55494379	GM12878	blood:	n/a	n/a
25	POLR2A	chr14:55493350-55494453	Hela-S3	cervix:	n/a	n/a
26	MTA3	chr14:55493350-55494561	GM12878	blood:	n/a	n/a
27	MXI1	chr14:55492547-55495304	SK-N-SH	brain:	n/a	n/a
28	TBP	chr14:55493357-55494496	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr14:55493302-55494470	Hela-S3	cervix:	n/a	chr14:55493833-55493842 chr14:55493337-55493346 chr14:55493338-55493347
30	POLR2A	chr14:55493186-55494212	MCF10A-Er-Src	breast:	n/a	n/a
31	MAFK	chr14:55493185-55493959	HepG2	liver:	n/a	n/a
32	POLR2A	chr14:55493402-55494484	GM12878	blood:	n/a	n/a
33	POLR2A	chr14:55493172-55494496	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr14:55493194-55494579	IMR90	lung:	n/a	n/a
35	POLR2A	chr14:55493399-55494393	MCF-7	breast:	n/a	n/a
36	TCF12	chr14:55493391-55494478	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr14:55493316-55494348	K562	blood:	n/a	n/a
38	POLR2A	chr14:55493287-55494582	GM12891	blood:	n/a	n/a
39	MAX	chr14:55493246-55494538	A549	lung:	n/a	chr14:55493833-55493842 chr14:55493337-55493346 chr14:55493338-55493347
40	CREB1	chr14:55493386-55494429	GM12878	blood:	n/a	n/a
41	E2F4	chr14:55493068-55494109	MCF10A-Er-Src	breast:	n/a	chr14:55493786-55493797 chr14:55493818-55493827
42	MAX	chr14:55493300-55494360	NB4	blood:	n/a	chr14:55493833-55493842 chr14:55493337-55493346 chr14:55493338-55493347
43	TCF12	chr14:55493313-55494564	A549	lung:	n/a	n/a
44	SRF	chr14:55493361-55494477	MCF-7	breast:	n/a	n/a
45	POLR2A	chr14:55493330-55494257	PFSK-1	brain:	n/a	n/a
46	SIN3A	chr14:55492237-55494788	H1-hESC	embryonic stem cell:	n/a	n/a
47	FOS	chr14:55493249-55493447	MCF10A-Er-Src	breast:	n/a	chr14:55493336-55493343 chr14:55493334-55493345 chr14:55493338-55493347 chr14:55493338-55493346 chr14:55493339-55493346
48	POLR2A	chr14:55493335-55494531	U87	brain:	n/a	n/a
49	EGR1	chr14:55493290-55494439	HCT-116	colon:	n/a	chr14:55493830-55493845 chr14:55493831-55493844 chr14:55493831-55493844 chr14:55493832-55493841 chr14:55493831-55493844 chr14:55493830-55493844 chr14:55493832-55493843 chr14:55494224-55494234 chr14:55493828-55493842 chr14:55493832-55493843 chr14:55494033-55494046 chr14:55493832-55493842 chr14:55493831-55493844 chr14:55493832-55493842 chr14:55493818-55493827
50	TAF1	chr14:55493199-55494531	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55490790..55495805-chr14:55515486..55522658,19	MCF-7	breast:
2	chr1:16840039..16840986-chr14:55493285..55494113,2	Hela-S3	cervix:
3	chr1:17231023..17232250-chr14:55493199..55494239,3	Hela-S3	cervix:
4	chr14:55491083..55496744-chr14:55514437..55523536,23	MCF-7	breast:
5	chr14:55492412..55494140-chr14:55594962..55596941,2	MCF-7	breast:
6	chr14:55491921..55500295-chr14:55515389..55520812,24	K562	blood:
7	chr14:55491992..55498342-chr14:55515529..55520367,21	K562	blood:

Variant related genes	Relation type
SOCS4	TF binding region
ENSG00000272426	Chromatin interaction
ENSG00000168175	Chromatin interaction
ENSG00000206652	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]
rs1209087	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
rs1201378	ATG14	cis	parietal	SCAN
rs1201378	FBXO34	cis	cerebellum	SCAN
rs1201378	MUDENG	cis	parietal	SCAN
rs1201378	WDHD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55491200-55495800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr14:55491400-55495200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr14:55491400-55495200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr14:55492000-55496200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:55492000-55496400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr14:55492200-55493600	Flanking Active TSS	HUVEC	blood vessel
7	chr14:55492200-55495200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr14:55492200-55495200	Active TSS	Brain Germinal Matrix	brain
9	chr14:55492200-55496000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:55492400-55493600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr14:55492400-55494800	Active TSS	Fetal Thymus	thymus
12	chr14:55492400-55495200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:55492400-55495200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:55492400-55495600	Active TSS	Fetal Kidney	kidney
15	chr14:55492400-55496800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr14:55492600-55493800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr14:55492600-55495000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:55492600-55495200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:55492600-55495200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:55492600-55495200	Active TSS	Fetal Muscle Trunk	muscle
21	chr14:55492600-55495400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr14:55492600-55495400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr14:55492600-55495800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr14:55492800-55493600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr14:55492800-55493600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr14:55492800-55493600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr14:55492800-55493600	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr14:55492800-55493600	Flanking Active TSS	Rectal Smooth Muscle	rectum
29	chr14:55492800-55493800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr14:55492800-55494400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr14:55492800-55494800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr14:55492800-55494800	Active TSS	Thymus	Thymus
33	chr14:55492800-55495000	Active TSS	Placenta Amnion	Placenta Amnion
34	chr14:55492800-55495400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr14:55492800-55495400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr14:55492800-55496400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:55492800-55496600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr14:55492800-55498400	Active TSS	GM12878-XiMat	blood
39	chr14:55493000-55493600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:55493000-55493600	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr14:55493000-55493600	Flanking Active TSS	Brain Substantia Nigra	brain
42	chr14:55493000-55493600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr14:55493000-55493800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr14:55493000-55493800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
45	chr14:55493000-55494800	Active TSS	Psoas Muscle	Psoas
46	chr14:55493000-55495000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr14:55493000-55495200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr14:55493000-55495200	Active TSS	Primary T cells fromperipheralblood	blood
49	chr14:55493000-55495200	Active TSS	Fetal Muscle Leg	muscle
50	chr14:55493000-55495200	Active TSS	HepG2	liver

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