Variant report

Variant	rs56378871
Chromosome Location	chr19:36905554-36905555
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	chr19:36884346..36886585-chr19:36904076..36906046,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12461529	0.88[ASN][1000 genomes]
rs12462725	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17206379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271842	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385802	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2857	0.88[ASN][1000 genomes]
rs2945955	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945956	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945989	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967508	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967511	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967516	0.82[ASN][1000 genomes]
rs2967519	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3098393	0.88[ASN][1000 genomes]
rs3111555	0.81[ASN][1000 genomes]
rs3111556	0.88[ASN][1000 genomes]
rs3810326	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61706074	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112567	0.88[ASN][1000 genomes]
rs62112568	0.88[ASN][1000 genomes]
rs62112569	0.88[ASN][1000 genomes]
rs62112624	0.88[ASN][1000 genomes]
rs62112631	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62112632	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62113869	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7253122	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73043845	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73043902	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104241	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1066026	chr19:36878441-36947928	ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv1067101	chr19:36901010-36956251	ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs56378871	LINC00665	cis	Muscle Skeletal	GTEx
rs56378871	LINC00665	cis	Nerve Tibial	GTEx
rs56378871	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs56378871	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36882200-36908800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:36882400-36907600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:36885600-36908000	Weak transcription	K562	blood
4	chr19:36889800-36908200	Weak transcription	HepG2	liver
5	chr19:36891800-36908200	Weak transcription	Fetal Heart	heart
6	chr19:36891800-36908200	Weak transcription	Hela-S3	cervix
7	chr19:36895000-36908200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:36896600-36908200	Weak transcription	Right Ventricle	heart
9	chr19:36896600-36908400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr19:36897200-36908200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:36898400-36906800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:36898400-36908600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
13	chr19:36899000-36908200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr19:36899200-36908400	Weak transcription	NH-A	brain
15	chr19:36899800-36905600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:36899800-36908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr19:36900000-36908200	Weak transcription	HUVEC	blood vessel
18	chr19:36900400-36908200	Weak transcription	Brain Substantia Nigra	brain
19	chr19:36900400-36908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:36900600-36908000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:36900800-36908200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr19:36900800-36908400	Weak transcription	Small Intestine	intestine
23	chr19:36901000-36907400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr19:36901000-36908000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr19:36901000-36908000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:36901000-36908400	Weak transcription	Fetal Kidney	kidney
27	chr19:36901000-36908400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr19:36901000-36908400	Weak transcription	HSMMtube	muscle
29	chr19:36901200-36908000	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:36901200-36908000	Weak transcription	Colon Smooth Muscle	Colon
31	chr19:36901200-36908200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:36901200-36908200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr19:36901200-36908200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr19:36901200-36908200	Weak transcription	Thymus	Thymus
35	chr19:36901200-36908400	Weak transcription	Colonic Mucosa	Colon
36	chr19:36901200-36908400	Weak transcription	Pancreas	Pancrea
37	chr19:36901200-36908400	Weak transcription	NHDF-Ad	bronchial
38	chr19:36901400-36908200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:36901400-36908200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:36901400-36908400	Weak transcription	Placenta	Placenta
41	chr19:36901800-36908400	Weak transcription	Left Ventricle	heart
42	chr19:36902000-36907600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr19:36902200-36905600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:36903200-36907400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr19:36903400-36906000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:36903400-36906000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:36903400-36907400	ZNF genes & repeats	Fetal Brain Female	brain
48	chr19:36903600-36906600	ZNF genes & repeats	Fetal Muscle Leg	muscle
49	chr19:36903800-36908000	Weak transcription	Adipose Nuclei	Adipose
50	chr19:36903800-36908200	Weak transcription	Rectal Smooth Muscle	rectum

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