Variant report

Variant	rs10427117
Chromosome Location	chr19:40501915-40501916
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	NRF1	chr19:40501772-40503798	SK-N-SH	brain:	n/a	chr19:40502894-40502908 chr19:40502897-40502908 chr19:40502897-40502908
2	MAX	chr19:40501659-40503808	A549	lung:	n/a	chr19:40502187-40502196
3	MAX	chr19:40501779-40503635	A549	lung:	n/a	chr19:40502187-40502196
4	SIX5	chr19:40501904-40503829	A549	lung:	n/a	chr19:40502942-40502951 chr19:40502938-40502952 chr19:40502940-40502949
5	SIN3AK20	chr19:40501400-40504621	PANC-1	pancreas:	n/a	n/a
6	SIN3AK20	chr19:40501266-40504472	PANC-1	pancreas:	n/a	n/a
7	NR3C1	chr19:40501691-40501966	A549	lung:	n/a	n/a
8	SP1	chr19:40501913-40503602	A549	lung:	n/a	n/a
9	POLR2A	chr19:40501602-40504091	IMR90	lung:	n/a	n/a
10	MXI1	chr19:40501820-40503750	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr19:40501794-40503545	MCF10A-Er-Src	breast:	n/a	n/a
12	NR3C1	chr19:40501706-40502084	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40497251..40499736-chr19:40500341..40503901,5	K562	blood:
2	chr19:40496278..40498751-chr19:40500341..40502344,2	K562	blood:
3	chr19:40475224..40479165-chr19:40500138..40503908,5	MCF-7	breast:
4	chr19:40475223..40478471-chr19:40501440..40504433,4	MCF-7	breast:
5	chr19:40474074..40479560-chr19:40500872..40505885,15	K562	blood:
6	chr19:40471803..40479510-chr19:40500414..40506141,13	K562	blood:
7	chr14:91976300..91976912-chr19:40501886..40502806,2	Hela-S3	cervix:
8	chr19:40497431..40499811-chr19:40501721..40503252,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF780B-2	chr19:40497983-40502942	NONHSAT066331

Variant related genes	Relation type
ZNF546	TF binding region
ENSG00000221233	TF binding region
ENSG00000100796	Chromatin interaction
ENSG00000221233	Chromatin interaction
ENSG00000013275	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10403646	1.00[AMR][1000 genomes]
rs10410695	1.00[EUR][1000 genomes]
rs10418448	1.00[EUR][1000 genomes]
rs10419218	1.00[EUR][1000 genomes]
rs10420514	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10420687	1.00[EUR][1000 genomes]
rs10421243	1.00[EUR][1000 genomes]
rs10423298	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10423800	1.00[EUR][1000 genomes]
rs11883159	1.00[EUR][1000 genomes]
rs13382054	1.00[EUR][1000 genomes]
rs170898	1.00[EUR][1000 genomes]
rs234297	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234307	1.00[EUR][1000 genomes]
rs234312	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234316	1.00[EUR][1000 genomes]
rs234319	1.00[EUR][1000 genomes]
rs234321	1.00[EUR][1000 genomes]
rs234322	1.00[EUR][1000 genomes]
rs234327	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs234339	1.00[EUR][1000 genomes]
rs234342	1.00[EUR][1000 genomes]
rs2542302	1.00[ASW][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28661993	1.00[EUR][1000 genomes]
rs28776318	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28832070	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs337795	1.00[EUR][1000 genomes]
rs57342065	1.00[EUR][1000 genomes]
rs58348431	1.00[EUR][1000 genomes]
rs59707868	1.00[EUR][1000 genomes]
rs60631264	1.00[EUR][1000 genomes]
rs61424085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245930	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250945	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258111	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7258718	1.00[AMR][1000 genomes]
rs73930675	1.00[EUR][1000 genomes]
rs73930678	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930679	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111518	1.00[EUR][1000 genomes]
rs8111741	1.00[EUR][1000 genomes]
rs9630860	1.00[EUR][1000 genomes]
rs9630868	1.00[EUR][1000 genomes]
rs9783944	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40490200-40502400	Weak transcription	Aorta	Aorta
2	chr19:40491000-40502200	Weak transcription	Ovary	ovary
3	chr19:40496600-40502200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr19:40500200-40502000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr19:40500200-40502200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:40500200-40502200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:40500400-40502200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:40500800-40502200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:40501000-40502200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr19:40501400-40502200	Enhancers	Pancreas	Pancrea
11	chr19:40501400-40502200	Enhancers	Thymus	Thymus
12	chr19:40501600-40502000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:40501600-40502000	Flanking Active TSS	Hela-S3	cervix
14	chr19:40501600-40502000	Flanking Active TSS	HepG2	liver
15	chr19:40501600-40502200	Enhancers	Primary B cells from cord blood	blood
16	chr19:40501600-40502200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:40501600-40502200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:40501600-40502400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr19:40501600-40502400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:40501600-40502400	Flanking Active TSS	Dnd41	blood
21	chr19:40501600-40502600	Active TSS	HMEC	breast
22	chr19:40501600-40503000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr19:40501600-40503200	Active TSS	Fetal Brain Female	brain
24	chr19:40501600-40503200	Active TSS	NHEK	skin
25	chr19:40501600-40503200	Active TSS	NHLF	lung
26	chr19:40501600-40503400	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr19:40501600-40503400	Active TSS	A549	lung
28	chr19:40501600-40503600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:40501800-40502000	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:40501800-40502000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:40501800-40502000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:40501800-40502000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr19:40501800-40502000	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr19:40501800-40502000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:40501800-40502000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:40501800-40502000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:40501800-40502000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:40501800-40502000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr19:40501800-40502000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:40501800-40502000	Flanking Active TSS	Liver	Liver
41	chr19:40501800-40502000	Enhancers	Brain Angular Gyrus	brain
42	chr19:40501800-40502000	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr19:40501800-40502000	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr19:40501800-40502000	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr19:40501800-40502000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr19:40501800-40502000	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr19:40501800-40502000	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr19:40501800-40502000	Flanking Active TSS	Fetal Kidney	kidney
49	chr19:40501800-40502000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr19:40501800-40502000	Flanking Active TSS	Fetal Lung	lung

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