Variant report

Variant	rs1946944
Chromosome Location	chr8:96102725-96102726
allele	A/C
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	chr8:96102528-96102979	K562	blood:	n/a	n/a
2	RUNX3	chr8:96101681-96103037	GM12878	blood:	n/a	n/a
3	STAT5A	chr8:96101823-96103030	GM12878	blood:	n/a	chr8:96101933-96101941 chr8:96102479-96102487
4	SPI1	chr8:96102629-96102851	K562	blood:	n/a	n/a
5	RELA	chr8:96101822-96102791	GM12878	blood:	n/a	chr8:96102052-96102061 chr8:96102052-96102061
6	ATF2	chr8:96101699-96102919	GM12878	blood:	n/a	n/a
7	JUND	chr8:96102492-96103096	SK-N-SH	brain:	n/a	chr8:96102779-96102787 chr8:96102780-96102787
8	RUNX3	chr8:96101697-96103225	GM12878	blood:	n/a	n/a
9	SMC3	chr8:96102534-96102818	K562	blood:	n/a	n/a
10	IRF1	chr8:96102264-96103114	K562	blood:	n/a	chr8:96102447-96102456 chr8:96102495-96102512
11	E2F4	chr8:96102623-96102924	MCF10A-Er-Src	breast:	n/a	n/a
12	EP300	chr8:96102655-96102934	SK-N-SH_RA	brain:	n/a	n/a
13	FOXM1	chr8:96101938-96102868	GM12878	blood:	n/a	n/a
14	GATA3	chr8:96102488-96103123	SK-N-SH	brain:	n/a	chr8:96102760-96102777 chr8:96102795-96102805
15	TBL1XR1	chr8:96102471-96103012	K562	blood:	n/a	n/a
16	POLR2A	chr8:96102617-96102923	SK-N-SH	brain:	n/a	n/a
17	MEF2A	chr8:96101907-96102824	GM12878	blood:	n/a	chr8:96102073-96102094 chr8:96102078-96102087 chr8:96102074-96102090 chr8:96102075-96102089 chr8:96102077-96102088 chr8:96102073-96102094 chr8:96102075-96102090
18	BACH1	chr8:96102586-96102974	K562	blood:	n/a	n/a
19	PML	chr8:96101695-96104710	GM12878	blood:	n/a	chr8:96102328-96102336
20	TCF12	chr8:96102427-96103142	SK-N-SH	brain:	n/a	n/a
21	IRF1	chr8:96102286-96102917	K562	blood:	n/a	chr8:96102447-96102456 chr8:96102495-96102512
22	UBTF	chr8:96102436-96102950	K562	blood:	n/a	n/a
23	MAX	chr8:96102191-96102897	K562	blood:	n/a	n/a
24	TEAD4	chr8:96102316-96103023	K562	blood:	n/a	chr8:96102503-96102512
25	POLR2A	chr8:96102442-96103142	K562	blood:	n/a	n/a
26	POLR2A	chr8:96102490-96102968	K562	blood:	n/a	n/a
27	STAT3	chr8:96102601-96102953	MCF10A-Er-Src	breast:	n/a	n/a
28	JUN	chr8:96102528-96102983	K562	blood:	n/a	chr8:96102779-96102787 chr8:96102780-96102787
29	POLR2A	chr8:96102317-96103211	GM12891	blood:	n/a	n/a
30	POLR2A	chr8:96101718-96104035	GM12878	blood:	n/a	n/a
31	MAZ	chr8:96102320-96103012	K562	blood:	n/a	n/a
32	FOS	chr8:96102581-96102977	HUVEC	blood vessel:	n/a	chr8:96102777-96102788 chr8:96102779-96102787 chr8:96102780-96102787
33	CBX3	chr8:96102385-96102920	K562	blood:	n/a	n/a
34	RELA	chr8:96101865-96102937	GM18951	blood:	n/a	chr8:96102052-96102061 chr8:96102052-96102061
35	STAT3	chr8:96102595-96102958	MCF10A-Er-Src	breast:	n/a	n/a
36	CHD1	chr8:96102013-96102902	GM12878	blood:	n/a	n/a
37	FOXM1	chr8:96101695-96103062	GM12878	blood:	n/a	n/a
38	POLR2A	chr8:96101910-96103184	GM12878	blood:	n/a	n/a
39	POLR2A	chr8:96102622-96103167	K562	blood:	n/a	n/a
40	EGR1	chr8:96102630-96102921	K562	blood:	n/a	n/a
41	SRF	chr8:96102577-96102863	K562	blood:	n/a	n/a
42	IRF1	chr8:96102171-96102959	K562	blood:	n/a	chr8:96102447-96102456 chr8:96102495-96102512
43	RCOR1	chr8:96102210-96103004	K562	blood:	n/a	n/a
44	CUX1	chr8:96101829-96103085	K562	blood:	n/a	n/a
45	JUN	chr8:96102562-96102975	HUVEC	blood vessel:	n/a	chr8:96102779-96102787 chr8:96102780-96102787
46	PML	chr8:96101983-96102928	GM12878	blood:	n/a	chr8:96102328-96102336
47	CBX3	chr8:96102165-96103174	K562	blood:	n/a	n/a
48	GATA2	chr8:96102432-96103204	K562	blood:	n/a	chr8:96102760-96102777 chr8:96102795-96102805 chr8:96102445-96102455
49	MAX	chr8:96102659-96102881	K562	blood:	n/a	n/a
50	GATA2	chr8:96102493-96102963	HUVEC	blood vessel:	n/a	chr8:96102760-96102777 chr8:96102795-96102805

No.	Distal block	Cell Line	Cell type
1	chr8:96100209..96105308-chr8:96143573..96151809,12	K562	blood:
2	chr8:96095758..96103345-chr8:96144049..96152228,17	MCF-7	breast:
3	chr8:96092840..96095684-chr8:96102296..96104588,4	K562	blood:
4	chr8:96095732..96098927-chr8:96100479..96105447,7	K562	blood:
5	chr8:96102152..96104618-chr8:96259174..96260844,2	K562	blood:
6	chr8:96102685..96105358-chr8:96146565..96148952,2	K562	blood:
7	chr8:96036531..96038925-chr8:96102648..96104628,2	K562	blood:
8	chr8:96078349..96080804-chr8:96101841..96104257,3	K562	blood:
9	chr8:96073662..96075442-chr8:96100722..96102763,2	K562	blood:
10	chr8:96100801..96102864-chr8:96280312..96283160,2	K562	blood:
11	chr8:96102212..96104143-chr8:96108955..96110574,2	K562	blood:

Variant related genes	Relation type
ENSG00000254248	TF binding region
ENSG00000175895	Chromatin interaction
ENSG00000156172	Chromatin interaction
ENSG00000156170	Chromatin interaction
ENSG00000253773	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1000285	0.82[CHB][hapmap]
rs1000286	0.82[CHB][hapmap]
rs10093559	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs10096848	0.82[CHB][hapmap]
rs11776488	0.82[CHB][hapmap]
rs11781134	1.00[CHB][hapmap]
rs11781447	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11782155	0.82[CHB][hapmap]
rs11784746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12543421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12548426	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13248868	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13251032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13251759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13273307	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13274368	1.00[ASN][1000 genomes]
rs13276227	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1451711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1451712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1946943	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119588	0.92[ASW][hapmap]
rs2341400	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34901613	0.97[ASN][1000 genomes]
rs4236831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4321970	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4323439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4329243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4540384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6471513	1.00[ASW][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6471520	0.84[TSI][hapmap]
rs6987762	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7008347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv891205	chr8:96062601-96115476	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
5	nsv891206	chr8:96092251-96115476	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1946944	PLEKHF2	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96098600-96111600	Weak transcription	Pancreas	Pancrea
2	chr8:96098800-96103800	Weak transcription	HepG2	liver
3	chr8:96100000-96104200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr8:96100400-96103200	Enhancers	NHEK	skin
5	chr8:96100400-96108000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:96100400-96113600	Weak transcription	Lung	lung
7	chr8:96100600-96103800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr8:96100600-96106800	Weak transcription	Spleen	Spleen
9	chr8:96100600-96112000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr8:96100800-96104600	Weak transcription	Placenta	Placenta
11	chr8:96100800-96104800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr8:96100800-96107600	Weak transcription	Hela-S3	cervix
13	chr8:96100800-96111800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr8:96101800-96102800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr8:96101800-96102800	Flanking Active TSS	K562	blood
16	chr8:96101800-96103000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr8:96101800-96103000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr8:96101800-96103000	Enhancers	NH-A	brain
19	chr8:96101800-96103000	Enhancers	Osteobl	bone
20	chr8:96101800-96103200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:96101800-96103200	Flanking Active TSS	GM12878-XiMat	blood
22	chr8:96101800-96103200	Enhancers	HUVEC	blood vessel
23	chr8:96101800-96103400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr8:96101800-96104200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr8:96102000-96102800	Enhancers	Primary hematopoietic stem cells	blood
26	chr8:96102000-96103000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr8:96102000-96103000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:96102000-96103200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr8:96102000-96103600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr8:96102000-96106600	Enhancers	Primary B cells from cord blood	blood
31	chr8:96102000-96107400	Enhancers	Primary B cells from peripheral blood	blood
32	chr8:96102200-96102800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr8:96102200-96102800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr8:96102200-96102800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr8:96102200-96103000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr8:96102200-96103000	Enhancers	Thymus	Thymus
37	chr8:96102200-96103200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr8:96102200-96103600	Enhancers	Fetal Thymus	thymus
39	chr8:96102400-96102800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr8:96102400-96102800	Enhancers	A549	lung
41	chr8:96102400-96102800	Enhancers	Dnd41	blood
42	chr8:96102400-96103000	Enhancers	Primary T cells fromperipheralblood	blood
43	chr8:96102400-96103000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr8:96102400-96103000	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr8:96102400-96103000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr8:96102400-96103000	Enhancers	HMEC	breast
47	chr8:96102400-96103200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr8:96102400-96103200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr8:96102400-96103200	Enhancers	Stomach Mucosa	stomach
50	chr8:96102400-96107600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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