Variant report

Variant	rs4805162
Chromosome Location	chr19:36674305-36674306
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	chr19:36630495..36633195-chr19:36673686..36676054,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10401633	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10402039	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10402069	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10402367	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10403200	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10405169	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409235	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410837	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10420462	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10426507	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1476504	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1559258	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974843	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2070132	0.81[MEX][hapmap]
rs2112971	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4372806	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4630678	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806282	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7249719	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258520	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103261	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv579425	chr19:36643695-36685753	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4805162	LTBP4	cis	parietal	SCAN
rs4805162	ACTN4	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36653200-36681400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:36653200-36684600	Weak transcription	Aorta	Aorta
3	chr19:36661800-36684600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:36661800-36686800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:36662000-36684800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:36669200-36685000	Weak transcription	Stomach Mucosa	stomach
7	chr19:36669600-36704800	Weak transcription	Psoas Muscle	Psoas
8	chr19:36672800-36678200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr19:36673000-36674600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:36673000-36674600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr19:36673000-36674600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:36673000-36674600	Strong transcription	Fetal Intestine Small	intestine
13	chr19:36673200-36674400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr19:36673200-36674400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:36673200-36674400	Strong transcription	Fetal Intestine Large	intestine
16	chr19:36673200-36674600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:36673200-36674600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:36673200-36674600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:36673200-36674600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr19:36673200-36674600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:36673200-36674600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:36673200-36674600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:36673200-36674600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:36673200-36674600	Strong transcription	Adipose Nuclei	Adipose
25	chr19:36673200-36674600	Strong transcription	Liver	Liver
26	chr19:36673200-36674600	Strong transcription	Brain Cingulate Gyrus	brain
27	chr19:36673200-36674600	Strong transcription	Brain Germinal Matrix	brain
28	chr19:36673200-36674600	Strong transcription	Brain Hippocampus Middle	brain
29	chr19:36673200-36674600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr19:36673200-36674600	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr19:36673200-36674600	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr19:36673200-36674600	ZNF genes & repeats	A549	lung
33	chr19:36673200-36674600	ZNF genes & repeats	HSMM	muscle
34	chr19:36673200-36674600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr19:36673200-36674600	Strong transcription	Osteobl	bone
36	chr19:36673400-36674400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr19:36673400-36674400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:36673400-36674400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:36673400-36674400	Strong transcription	Fetal Brain Male	brain
40	chr19:36673400-36674400	Strong transcription	Left Ventricle	heart
41	chr19:36673400-36674400	Strong transcription	Lung	lung
42	chr19:36673400-36674400	Strong transcription	Rectal Smooth Muscle	rectum
43	chr19:36673400-36674400	Strong transcription	HUVEC	blood vessel
44	chr19:36673400-36674400	ZNF genes & repeats	NHLF	lung
45	chr19:36673400-36674600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr19:36673400-36674600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:36673400-36674600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:36673400-36674600	Enhancers	HUES64 Cell Line	embryonic stem cell
49	chr19:36673400-36674600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:36673400-36674600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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