Variant report

Variant	rs6847139
Chromosome Location	chr4:87465741-87465742
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	IKZF1	chr4:87465082-87466315	GM12878	blood:	n/a	n/a
2	EP300	chr4:87465159-87466062	GM12878	blood:	n/a	chr4:87466031-87466045 chr4:87466029-87466043
3	BCL11A	chr4:87465487-87465809	GM12878	blood:	n/a	n/a
4	MAFK	chr4:87465396-87466135	HepG2	liver:	n/a	chr4:87465956-87465972 chr4:87465959-87465975 chr4:87465956-87465971 chr4:87465909-87465924 chr4:87465517-87465537 chr4:87465960-87465974 chr4:87465520-87465534 chr4:87465516-87465531 chr4:87465515-87465529 chr4:87465519-87465535 chr4:87465957-87465977 chr4:87465517-87465528
5	NFIC	chr4:87465466-87466156	GM12878	blood:	n/a	n/a
6	ZNF384	chr4:87465420-87466336	GM12878	blood:	n/a	n/a
7	NFIC	chr4:87465249-87466239	GM12878	blood:	n/a	n/a
8	BCLAF1	chr4:87465387-87465935	GM12878	blood:	n/a	chr4:87465873-87465880
9	RUNX3	chr4:87465223-87466191	GM12878	blood:	n/a	chr4:87465481-87465490 chr4:87465481-87465490
10	CUX1	chr4:87465491-87466149	GM12878	blood:	n/a	n/a
11	TBP	chr4:87465476-87466114	GM12878	blood:	n/a	n/a
12	IRF4	chr4:87465382-87465814	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:87465733-87466203	SK-N-MC	brain:	n/a	n/a
14	NFYB	chr4:87465475-87465880	GM12878	blood:	n/a	n/a
15	STAT3	chr4:87465447-87465858	GM12878	blood:	n/a	n/a
16	EP300	chr4:87465374-87466165	GM12878	blood:	n/a	chr4:87466031-87466045 chr4:87466029-87466043
17	RUNX3	chr4:87465380-87466126	GM12878	blood:	n/a	chr4:87465481-87465490 chr4:87465481-87465490
18	RCOR1	chr4:87465397-87466316	GM12878	blood:	n/a	n/a
19	ATF2	chr4:87465369-87465993	GM12878	blood:	n/a	n/a
20	TBL1XR1	chr4:87465481-87466026	GM12878	blood:	n/a	n/a
21	BATF	chr4:87465431-87465798	GM12878	blood:	n/a	chr4:87465625-87465634
22	ATF2	chr4:87465369-87466161	GM12878	blood:	n/a	n/a
23	EBF1	chr4:87465548-87465742	GM12878	blood:	n/a	n/a
24	MXI1	chr4:87465382-87466258	GM12878	blood:	n/a	n/a
25	FOXM1	chr4:87465323-87466183	GM12878	blood:	n/a	n/a
26	BHLHE40	chr4:87465476-87466320	GM12878	blood:	n/a	n/a
27	MAFK	chr4:87465366-87466102	IMR90	lung:	n/a	chr4:87465956-87465972 chr4:87465959-87465975 chr4:87465956-87465971 chr4:87465909-87465924 chr4:87465517-87465537 chr4:87465960-87465974 chr4:87465520-87465534 chr4:87465516-87465531 chr4:87465515-87465529 chr4:87465519-87465535 chr4:87465957-87465977 chr4:87465517-87465528
28	CEBPB	chr4:87465313-87466285	GM12878	blood:	n/a	chr4:87466220-87466233

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87464603..87467042-chr4:87514125..87517008,2	MCF-7	breast:

Variant related genes	Relation type
MIR4452	TF binding region
ENSG00000163629	Chromatin interaction
ENSG00000109339	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10008165	0.95[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs10023787	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10029671	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap]
rs10031843	0.89[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1021101	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs1026861	0.82[ASW][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap]
rs11097115	0.89[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11943428	0.82[ASN][1000 genomes]
rs11947018	0.84[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs11947775	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1481833	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17011924	0.90[ASN][1000 genomes]
rs17418221	0.85[ASN][1000 genomes]
rs17418531	0.91[ASN][1000 genomes]
rs17418801	0.93[ASN][1000 genomes]
rs17418878	0.94[ASN][1000 genomes]
rs17419295	0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs17419627	0.90[JPT][hapmap]
rs17419929	0.85[JPT][hapmap]
rs17452467	0.91[ASN][1000 genomes]
rs17452556	0.93[ASN][1000 genomes]
rs17453839	0.89[CHB][hapmap]
rs28483710	0.85[ASN][1000 genomes]
rs28485273	0.81[ASN][1000 genomes]
rs28529445	0.82[ASN][1000 genomes]
rs28534599	0.81[ASN][1000 genomes]
rs28663376	0.81[ASN][1000 genomes]
rs28735881	0.81[ASN][1000 genomes]
rs4235081	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277747	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4404513	0.92[ASN][1000 genomes]
rs4405982	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4407468	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4452393	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4466012	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4511966	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4513526	0.85[ASN][1000 genomes]
rs4529013	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4552430	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4607180	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4622964	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4640633	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693147	0.95[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs4693772	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693776	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4693777	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs55653332	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55654230	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55660529	0.94[ASN][1000 genomes]
rs55722156	0.93[ASN][1000 genomes]
rs55746316	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55757426	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55773619	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs55814693	0.82[ASN][1000 genomes]
rs55842318	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55872468	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55879246	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55881335	0.90[ASN][1000 genomes]
rs55908925	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55930543	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs55969415	0.91[ASN][1000 genomes]
rs55982489	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs56009992	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56150118	0.82[ASN][1000 genomes]
rs56164000	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56178389	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56222033	0.94[ASN][1000 genomes]
rs56296936	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56348925	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56353461	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59644743	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61152200	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6531932	0.95[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs66669421	0.81[ASN][1000 genomes]
rs67274037	0.81[ASN][1000 genomes]
rs67341369	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67523832	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67928053	0.85[ASN][1000 genomes]
rs6822396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6838659	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72664002	0.91[ASN][1000 genomes]
rs72665711	0.96[ASN][1000 genomes]
rs72665712	0.96[ASN][1000 genomes]
rs72665714	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72665719	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72665722	0.96[ASN][1000 genomes]
rs72665724	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72665725	0.96[ASN][1000 genomes]
rs72665729	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665734	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665736	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665737	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665738	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665744	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72665752	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72665753	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72665756	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72665759	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665762	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72665769	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72665771	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs72665772	0.82[ASN][1000 genomes]
rs72665777	0.81[ASN][1000 genomes]
rs7435744	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7673698	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7675845	0.88[ASN][1000 genomes]
rs7679269	0.82[ASN][1000 genomes]
rs7694723	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7695011	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697819	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9307020	0.89[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs9683663	0.93[ASN][1000 genomes]
rs9993042	0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1012836	chr4:87279206-87643558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	esv2757071	chr4:87417291-87689533	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2759264	chr4:87417291-87689533	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6847139	PTPN13	cis	parietal	SCAN
rs6847139	HPSE	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87443200-87468000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:87458000-87468200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:87459400-87468600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr4:87460600-87466600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:87461400-87466400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:87462600-87474000	Weak transcription	Ovary	ovary
7	chr4:87462600-87478000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:87463600-87466800	Enhancers	GM12878-XiMat	blood
9	chr4:87463800-87466200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr4:87463800-87466200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr4:87464000-87466200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:87464000-87466800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:87464000-87466800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr4:87464000-87467200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:87464400-87466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr4:87464400-87466200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:87464400-87466800	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr4:87464600-87465800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr4:87464600-87466400	Enhancers	Primary T cells from cord blood	blood
20	chr4:87464600-87466400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:87464800-87465800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:87464800-87466000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr4:87464800-87466000	Enhancers	NH-A	brain
24	chr4:87465000-87465800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr4:87465000-87465800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:87465000-87466400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:87465000-87466600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:87465000-87466600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:87465000-87467000	Enhancers	Dnd41	blood
30	chr4:87465200-87466000	Weak transcription	Brain Angular Gyrus	brain
31	chr4:87465200-87466200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:87465200-87466800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr4:87465200-87466800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr4:87465200-87467000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:87465200-87470400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:87465400-87465800	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr4:87465400-87466200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr4:87465400-87466400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:87465400-87469800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr4:87465400-87470800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:87465400-87472000	Weak transcription	Brain Anterior Caudate	brain
42	chr4:87465400-87473800	Weak transcription	HMEC	breast
43	chr4:87465600-87465800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr4:87465600-87466400	Enhancers	Primary hematopoietic stem cells	blood
45	chr4:87465600-87466400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr4:87465600-87470400	Weak transcription	Osteobl	bone

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