Variant report

Variant	rs2927488
Chromosome Location	chr19:45231478-45231479
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:45222394..45233722-chr19:45248498..45258065,33	MCF-7	breast:
2	chr19:45225977..45229146-chr19:45231463..45233615,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000069399	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10422350	0.80[ASN][1000 genomes]
rs17658713	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17728272	0.94[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2965102	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965103	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2965104	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2965105	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56702353	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56978169	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59170622	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8100239	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912116	chr19:45146103-45298069	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv833841	chr19:45208486-45308043	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
3	esv3335183	chr19:45225161-45253316	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2927488	C19orf73	cis	parietal	SCAN
rs2927488	IRF2BP1	cis	cerebellum	SCAN
rs2927488	ZNF613	cis	parietal	SCAN
rs2927488	BCL2L12	cis	cerebellum	SCAN
rs2927488	AKT1S1	cis	parietal	SCAN
rs2927488	OPA3	cis	parietal	SCAN
rs2927488	SIGLEC10	cis	cerebellum	SCAN
rs2927488	ZNF468	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45226000-45232400	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr19:45228800-45231600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr19:45229000-45232400	Enhancers	HepG2	liver
4	chr19:45229000-45240800	Weak transcription	Right Atrium	heart
5	chr19:45229200-45233000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:45229200-45238000	Weak transcription	Esophagus	oesophagus
7	chr19:45229200-45240800	Weak transcription	Spleen	Spleen
8	chr19:45229800-45234200	Weak transcription	Colonic Mucosa	Colon
9	chr19:45230000-45235200	Weak transcription	Stomach Mucosa	stomach
10	chr19:45230800-45231800	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:45230800-45232000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:45231000-45231600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:45231000-45231600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr19:45231000-45231600	Enhancers	Fetal Muscle Leg	muscle
15	chr19:45231000-45231800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr19:45231000-45232000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr19:45231000-45232000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:45231000-45232000	Enhancers	Fetal Muscle Trunk	muscle
19	chr19:45231000-45232200	Enhancers	Primary hematopoietic stem cells	blood
20	chr19:45231000-45232400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:45231000-45233000	Enhancers	GM12878-XiMat	blood
22	chr19:45231000-45233200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:45231000-45233600	Enhancers	Primary B cells from peripheral blood	blood
24	chr19:45231200-45231800	Enhancers	Primary B cells from cord blood	blood
25	chr19:45231200-45231800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr19:45231200-45231800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr19:45231200-45235600	Weak transcription	Fetal Thymus	thymus
28	chr19:45231400-45231600	Enhancers	Fetal Lung	lung
29	chr19:45231400-45232400	Enhancers	A549	lung
30	chr19:45231400-45234800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:45231400-45234800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:45231400-45238400	Weak transcription	Small Intestine	intestine
33	chr19:45231400-45240600	Weak transcription	Lung	lung

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