Variant report

Variant	rs1594842
Chromosome Location	chr14:39739324-39739325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr14:39739127-39739331	IMR90	lung:	n/a	n/a
2	MAFK	chr14:39739021-39739385	HepG2	liver:	n/a	n/a
3	STAT3	chr14:39739042-39739365	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr14:39739018-39739368	MCF10A-Er-Src	breast:	n/a	n/a
5	MAFK	chr14:39739056-39739363	K562	blood:	n/a	n/a
6	FOS	chr14:39739016-39739361	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr14:39739018-39739371	MCF10A-Er-Src	breast:	n/a	n/a
8	MAFK	chr14:39739122-39739391	H1-hESC	embryonic stem cell:	n/a	n/a
9	MAFK	chr14:39739031-39739398	HepG2	liver:	n/a	n/a
10	BACH1	chr14:39739052-39739364	K562	blood:	n/a	n/a
11	EBF1	chr14:39739121-39739406	GM12878	blood:	n/a	n/a
12	BACH1	chr14:39739148-39739379	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAFF	chr14:39739046-39739396	HepG2	liver:	n/a	n/a
14	STAT3	chr14:39739066-39739370	MCF10A-Er-Src	breast:	n/a	n/a
15	MAFF	chr14:39739067-39739372	K562	blood:	n/a	n/a
16	STAT3	chr14:39739065-39739367	MCF10A-Er-Src	breast:	n/a	n/a
17	RUNX3	chr14:39739136-39739522	GM12878	blood:	n/a	n/a
18	ZNF384	chr14:39739140-39739550	GM12878	blood:	n/a	n/a
19	FOS	chr14:39739026-39739361	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr14:39636108..39642775-chr14:39734196..39739360,12	MCF-7	breast:
2	chr14:39639538..39641336-chr14:39738634..39740819,2	MCF-7	breast:
3	chr14:39737724..39741488-chr14:39742832..39745249,3	K562	blood:
4	chr14:39652053..39654773-chr14:39736732..39739387,2	K562	blood:
5	chr14:39565337..39567780-chr14:39737837..39739519,2	MCF-7	breast:
6	chr14:39733456..39736427-chr14:39738159..39742075,4	K562	blood:
7	chr14:39733186..39738068-chr14:39738751..39742738,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258940	TF binding region
ENSG00000150527	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000182400	Chromatin interaction
ENSG00000258940	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10131617	0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10133417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10134143	0.87[ASN][1000 genomes]
rs10134365	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10137352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10137905	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs10138024	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10138869	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10151659	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10162550	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10872920	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs11157053	0.95[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs11157058	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11620695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11621264	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621330	0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11621822	0.88[ASN][1000 genomes]
rs11624839	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11626150	0.87[ASN][1000 genomes]
rs11626679	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11627580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11628075	0.86[ASN][1000 genomes]
rs11845046	0.89[ASN][1000 genomes]
rs12434140	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs12587713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12588386	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12588728	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12589831	0.88[ASN][1000 genomes]
rs12590172	0.80[JPT][hapmap]
rs12882709	0.88[ASN][1000 genomes]
rs12883781	0.80[ASN][1000 genomes]
rs12892482	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12894855	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs12894960	0.82[ASN][1000 genomes]
rs12896838	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17109021	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109028	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs17109056	0.89[ASN][1000 genomes]
rs17109073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17109100	0.80[ASN][1000 genomes]
rs1897792	0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs1950952	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs1998194	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2082635	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2274395	0.86[JPT][hapmap]
rs2274396	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap]
rs2274399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28626340	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28680827	0.86[ASN][1000 genomes]
rs35065854	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35184650	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35201135	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35613410	0.88[ASN][1000 genomes]
rs3814860	0.86[JPT][hapmap]
rs4902528	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs4902569	0.90[CEU][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs4902570	0.90[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs4902622	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4902648	0.82[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6571919	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7140164	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7143646	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7148150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7150735	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7152341	0.86[JPT][hapmap]
rs7153482	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs7161403	0.82[JPT][hapmap]
rs719455	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs8004348	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8004716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8006321	0.86[JPT][hapmap]
rs8018717	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs910370	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs956108	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs956109	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9671943	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9671953	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1594842	LRFN5	cis	cerebellum	SCAN
rs1594842	PPP2R3C	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39737000-39741000	Weak transcription	Spleen	Spleen
2	chr14:39737000-39751800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:39737200-39741600	Weak transcription	Esophagus	oesophagus
4	chr14:39737600-39739400	Flanking Active TSS	Hela-S3	cervix
5	chr14:39737800-39739400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
6	chr14:39737800-39739400	Enhancers	Small Intestine	intestine
7	chr14:39737800-39740000	Enhancers	Liver	Liver
8	chr14:39737800-39748800	Weak transcription	Right Ventricle	heart
9	chr14:39737800-39750800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:39737800-39763800	Weak transcription	Gastric	stomach
11	chr14:39738000-39739400	Enhancers	Primary hematopoietic stem cells	blood
12	chr14:39738000-39739800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr14:39738000-39739800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr14:39738000-39740000	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr14:39738000-39740400	Enhancers	Primary T cells from cord blood	blood
16	chr14:39738000-39740400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr14:39738000-39740600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr14:39738000-39740600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr14:39738000-39740800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr14:39738000-39740800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr14:39738000-39740800	Weak transcription	Brain Germinal Matrix	brain
22	chr14:39738000-39742400	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr14:39738000-39742600	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr14:39738000-39744400	Weak transcription	Right Atrium	heart
25	chr14:39738000-39748800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:39738000-39750600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr14:39738000-39752000	Weak transcription	Stomach Mucosa	stomach
28	chr14:39738000-39763800	Weak transcription	HSMM	muscle
29	chr14:39738200-39739400	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr14:39738200-39739400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr14:39738200-39739400	Enhancers	Pancreatic Islets	Pancreatic Islet
32	chr14:39738200-39739400	Enhancers	K562	blood
33	chr14:39738200-39739800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr14:39738200-39739800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr14:39738200-39739800	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr14:39738200-39739800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr14:39738200-39740000	Enhancers	Dnd41	blood
38	chr14:39738200-39740200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr14:39738200-39741000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr14:39738200-39741000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:39738200-39741000	Weak transcription	Fetal Stomach	stomach
42	chr14:39738200-39742000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr14:39738200-39745000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:39738200-39747000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr14:39738200-39748800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr14:39738200-39748800	Weak transcription	Fetal Kidney	kidney
47	chr14:39738200-39748800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr14:39738200-39748800	Weak transcription	Osteobl	bone
49	chr14:39738200-39751800	Weak transcription	Colonic Mucosa	Colon
50	chr14:39738200-39751800	Weak transcription	Rectal Smooth Muscle	rectum

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