Variant report

Variant	rs10416241
Chromosome Location	chr19:42900253-42900254
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	MAX	chr19:42899884-42902339	A549	lung:	n/a	chr19:42900536-42900545 chr19:42901461-42901471 chr19:42899996-42900005
2	RFX5	chr19:42899800-42901883	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr19:42900196-42902225	A549	lung:	n/a	chr19:42900975-42900984
4	HDAC2	chr19:42899975-42900256	K562	blood:	n/a	chr19:42900229-42900243 chr19:42900228-42900242
5	GATA3	chr19:42900231-42900525	SH-SY5Y	brain:	n/a	n/a
6	SIX5	chr19:42899976-42901943	A549	lung:	n/a	n/a
7	BCL3	chr19:42900101-42902425	A549	lung:	n/a	n/a
8	JUN	chr19:42899374-42901964	K562	blood:	n/a	chr19:42899621-42899631 chr19:42901127-42901136
9	FOSL2	chr19:42900122-42901946	A549	lung:	n/a	chr19:42901127-42901136

No.	Distal block	Cell Line	Cell type
1	chr19:42900219..42901127-chr19:42923966..42924540,2	MCF-7	breast:
2	chr19:42894410..42896597-chr19:42899559..42901447,2	MCF-7	breast:
3	chr19:42816448..42818844-chr19:42899476..42901532,2	K562	blood:
4	chr19:42892157..42894353-chr19:42898582..42900321,2	MCF-7	breast:
5	chr19:42816534..42818844-chr19:42898709..42900976,2	K562	blood:
6	chr19:42785237..42787439-chr19:42898347..42900741,2	K562	blood:
7	chr19:42805304..42808319-chr19:42899510..42903078,3	K562	blood:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000079462	Chromatin interaction
ENSG00000105427	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000167619	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10401224	0.85[YRI][hapmap]
rs10403246	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs10406755	1.00[AMR][1000 genomes]
rs10408141	1.00[AMR][1000 genomes]
rs10409428	0.85[YRI][hapmap]
rs10409433	0.85[YRI][hapmap]
rs10410129	0.85[YRI][hapmap]
rs10410653	0.85[YRI][hapmap]
rs10412954	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10413484	0.85[YRI][hapmap]
rs10414056	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414620	0.92[YRI][hapmap];0.82[AFR][1000 genomes]
rs10415478	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10418493	1.00[AMR][1000 genomes]
rs10419013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10421409	0.85[YRI][hapmap]
rs10425883	1.00[ASW][hapmap];1.00[AMR][1000 genomes]
rs11880356	0.85[YRI][hapmap]
rs13343322	0.85[YRI][hapmap]
rs13343761	1.00[ASW][hapmap]
rs13345986	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28393692	1.00[AMR][1000 genomes]
rs28532592	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28572784	1.00[ASW][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs35620536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6509012	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7257090	1.00[AMR][1000 genomes]
rs7258727	0.85[YRI][hapmap]
rs73552850	1.00[AMR][1000 genomes]
rs8099885	0.85[YRI][hapmap]
rs8109258	0.85[YRI][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv911788	chr19:42887492-42930652	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42891800-42900800	Weak transcription	Right Atrium	heart
2	chr19:42893400-42900600	Weak transcription	Spleen	Spleen
3	chr19:42896200-42900800	Weak transcription	Esophagus	oesophagus
4	chr19:42896800-42900400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:42899000-42900400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:42899000-42900400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:42899400-42900400	Enhancers	K562	blood
8	chr19:42899400-42900600	Enhancers	Primary neutrophils fromperipheralblood	blood
9	chr19:42899400-42901200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:42899600-42900600	Enhancers	Adipose Nuclei	Adipose
11	chr19:42899600-42900600	Enhancers	Fetal Muscle Trunk	muscle
12	chr19:42899800-42900400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr19:42899800-42900400	Enhancers	Dnd41	blood
14	chr19:42899800-42900400	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr19:42899800-42900600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:42899800-42900600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr19:42899800-42900600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr19:42899800-42900600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:42899800-42900600	Enhancers	Duodenum Mucosa	Duodenum
20	chr19:42899800-42900600	Enhancers	Fetal Muscle Leg	muscle
21	chr19:42899800-42900600	Enhancers	Fetal Stomach	stomach
22	chr19:42900000-42900400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:42900000-42900400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr19:42900000-42900400	Enhancers	Brain Germinal Matrix	brain
25	chr19:42900000-42900600	Enhancers	Primary hematopoietic stem cells	blood
26	chr19:42900000-42900600	Flanking Active TSS	Hela-S3	cervix
27	chr19:42900200-42900400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:42900200-42900400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr19:42900200-42900400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr19:42900200-42900400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr19:42900200-42900400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr19:42900200-42900400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr19:42900200-42900400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr19:42900200-42900400	Enhancers	NHEK	skin
35	chr19:42900200-42900600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:42900200-42900800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:42900200-42900800	Enhancers	Fetal Heart	heart
38	chr19:42900200-42900800	Flanking Active TSS	A549	lung
39	chr19:42900200-42902200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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