Variant report

Variant	rs11672399
Chromosome Location	chr19:45377098-45377099
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:45348165..45354069-chr19:45369473..45378418,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130202	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10424663	1.00[CHB][hapmap]
rs11667640	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671274	0.86[EUR][1000 genomes]
rs11879589	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs17561351	0.83[EUR][1000 genomes]
rs3852857	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4081918	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs41290110	1.00[ASN][1000 genomes]
rs41290122	0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534183	chr19:45351707-45385809	Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11672399	PVRL2	cis	Whole Blood	GTEx
rs11672399	CTB-129P6.4	cis	Whole Blood	GTEx
rs11672399	PVRL2	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45354200-45382600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:45360400-45381800	Weak transcription	Psoas Muscle	Psoas
3	chr19:45367200-45378800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr19:45367200-45392200	Strong transcription	Fetal Stomach	stomach
5	chr19:45367400-45382400	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr19:45368000-45380400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr19:45368000-45381200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr19:45368000-45383400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr19:45368200-45379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:45368200-45379400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:45368200-45380000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:45368200-45382400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr19:45368200-45383400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:45368600-45380400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:45369800-45393000	Weak transcription	Brain Angular Gyrus	brain
16	chr19:45370000-45377800	Weak transcription	Fetal Thymus	thymus
17	chr19:45373000-45393000	Weak transcription	Fetal Brain Male	brain
18	chr19:45373400-45383400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr19:45373600-45377600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:45373600-45378200	Weak transcription	Brain Hippocampus Middle	brain
21	chr19:45373800-45377200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:45373800-45378400	Strong transcription	Fetal Intestine Large	intestine
23	chr19:45373800-45378800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:45373800-45383600	Strong transcription	Liver	Liver
25	chr19:45374000-45378800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:45374000-45378800	Strong transcription	HSMM	muscle
27	chr19:45374400-45377800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:45374400-45379600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr19:45374400-45380400	Strong transcription	Placenta Amnion	Placenta Amnion
30	chr19:45374400-45382200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:45374400-45383200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:45374400-45383800	Strong transcription	Stomach Smooth Muscle	stomach
33	chr19:45374600-45378200	Strong transcription	HUVEC	blood vessel
34	chr19:45374600-45379000	Strong transcription	Osteobl	bone
35	chr19:45374600-45379800	Strong transcription	Fetal Brain Female	brain
36	chr19:45374600-45380200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:45374600-45381800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:45374600-45382600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:45374600-45382800	Strong transcription	Brain Germinal Matrix	brain
40	chr19:45374600-45382800	Strong transcription	Ovary	ovary
41	chr19:45374800-45378200	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr19:45374800-45379000	Strong transcription	NHLF	lung
43	chr19:45374800-45381000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:45374800-45382000	Strong transcription	HepG2	liver
45	chr19:45374800-45382400	Strong transcription	Spleen	Spleen
46	chr19:45374800-45383200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:45374800-45383400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:45375000-45378200	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr19:45375000-45378800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr19:45375000-45378800	Strong transcription	Duodenum Mucosa	Duodenum

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