Variant report

Variant	rs10415999
Chromosome Location	chr19:42900125-42900126
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	HDAC2	chr19:42899975-42900256	K562	blood:	n/a	chr19:42900229-42900243 chr19:42900228-42900242
4	SIX5	chr19:42899976-42901943	A549	lung:	n/a	n/a
5	BCL3	chr19:42900101-42902425	A549	lung:	n/a	n/a
6	JUN	chr19:42899374-42901964	K562	blood:	n/a	chr19:42899621-42899631 chr19:42901127-42901136
7	FOSL2	chr19:42900122-42901946	A549	lung:	n/a	chr19:42901127-42901136

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

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

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10401224	1.00[EUR][1000 genomes]
rs10401235	0.84[AFR][1000 genomes]
rs10402438	1.00[EUR][1000 genomes]
rs10404650	1.00[EUR][1000 genomes]
rs10406972	1.00[EUR][1000 genomes]
rs10407085	1.00[EUR][1000 genomes]
rs10407155	1.00[EUR][1000 genomes]
rs10407842	1.00[EUR][1000 genomes]
rs10408258	1.00[EUR][1000 genomes]
rs10409428	1.00[EUR][1000 genomes]
rs10409433	1.00[EUR][1000 genomes]
rs10409939	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10410129	1.00[EUR][1000 genomes]
rs10410653	1.00[EUR][1000 genomes]
rs10410995	0.84[AMR][1000 genomes]
rs10411498	1.00[EUR][1000 genomes]
rs10411908	1.00[EUR][1000 genomes]
rs10413484	1.00[EUR][1000 genomes]
rs10416535	1.00[EUR][1000 genomes]
rs10418312	1.00[EUR][1000 genomes]
rs10418816	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10421409	1.00[EUR][1000 genomes]
rs10421510	1.00[EUR][1000 genomes]
rs10421857	1.00[EUR][1000 genomes]
rs10422301	1.00[EUR][1000 genomes]
rs10422867	1.00[EUR][1000 genomes]
rs10423812	1.00[EUR][1000 genomes]
rs10423959	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423978	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10424402	1.00[EUR][1000 genomes]
rs10425003	1.00[EUR][1000 genomes]
rs10425320	1.00[EUR][1000 genomes]
rs10425783	1.00[EUR][1000 genomes]
rs10426267	1.00[EUR][1000 genomes]
rs10426284	1.00[EUR][1000 genomes]
rs11878207	1.00[EUR][1000 genomes]
rs11878297	1.00[EUR][1000 genomes]
rs11879073	1.00[EUR][1000 genomes]
rs11879538	1.00[EUR][1000 genomes]
rs11880214	1.00[EUR][1000 genomes]
rs11880356	1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	1.00[EUR][1000 genomes]
rs13343388	1.00[EUR][1000 genomes]
rs13343719	1.00[EUR][1000 genomes]
rs13343761	1.00[EUR][1000 genomes]
rs13343834	1.00[EUR][1000 genomes]
rs13343966	1.00[EUR][1000 genomes]
rs13346837	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2229614	1.00[EUR][1000 genomes]
rs28463673	1.00[EUR][1000 genomes]
rs28469564	1.00[EUR][1000 genomes]
rs28474957	1.00[EUR][1000 genomes]
rs28483598	1.00[EUR][1000 genomes]
rs28496975	1.00[EUR][1000 genomes]
rs28657829	1.00[EUR][1000 genomes]
rs28663042	1.00[EUR][1000 genomes]
rs28675019	1.00[EUR][1000 genomes]
rs28675764	1.00[EUR][1000 genomes]
rs28699037	1.00[EUR][1000 genomes]
rs28711448	1.00[EUR][1000 genomes]
rs28715574	1.00[EUR][1000 genomes]
rs33919763	1.00[EUR][1000 genomes]
rs35707383	1.00[EUR][1000 genomes]
rs36089262	1.00[EUR][1000 genomes]
rs59870753	1.00[EUR][1000 genomes]
rs60950516	1.00[EUR][1000 genomes]
rs7246232	1.00[EUR][1000 genomes]
rs7248473	1.00[EUR][1000 genomes]
rs7254853	1.00[EUR][1000 genomes]
rs7255343	1.00[EUR][1000 genomes]
rs7258727	1.00[EUR][1000 genomes]
rs73552879	1.00[EUR][1000 genomes]
rs73554520	1.00[EUR][1000 genomes]
rs73554531	1.00[EUR][1000 genomes]
rs8099885	1.00[EUR][1000 genomes]
rs8109258	1.00[EUR][1000 genomes]
rs9304602	1.00[EUR][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	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:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42891800-42900800	Weak transcription	Right Atrium	heart
2	chr19:42892000-42900200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr19:42893400-42900600	Weak transcription	Spleen	Spleen
4	chr19:42896200-42900800	Weak transcription	Esophagus	oesophagus
5	chr19:42896800-42900400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:42899000-42900200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42899000-42900200	Enhancers	A549	lung
8	chr19:42899000-42900400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:42899000-42900400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:42899400-42900400	Enhancers	K562	blood
11	chr19:42899400-42900600	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr19:42899400-42901200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:42899600-42900600	Enhancers	Adipose Nuclei	Adipose
14	chr19:42899600-42900600	Enhancers	Fetal Muscle Trunk	muscle
15	chr19:42899800-42900200	Weak transcription	Fetal Heart	heart
16	chr19:42899800-42900400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr19:42899800-42900400	Enhancers	Dnd41	blood
18	chr19:42899800-42900400	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr19:42899800-42900600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:42899800-42900600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr19:42899800-42900600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:42899800-42900600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:42899800-42900600	Enhancers	Duodenum Mucosa	Duodenum
24	chr19:42899800-42900600	Enhancers	Fetal Muscle Leg	muscle
25	chr19:42899800-42900600	Enhancers	Fetal Stomach	stomach
26	chr19:42900000-42900200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr19:42900000-42900200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:42900000-42900400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:42900000-42900400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr19:42900000-42900400	Enhancers	Brain Germinal Matrix	brain
31	chr19:42900000-42900600	Enhancers	Primary hematopoietic stem cells	blood
32	chr19:42900000-42900600	Flanking Active TSS	Hela-S3	cervix

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