Variant report

Variant	rs6510526
Chromosome Location	chr19:36666296-36666297
allele	A/G
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	POLR2A	chr19:36666016-36666539	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:36666270-36666523	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:36666124-36666450	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36603757..36607457-chr19:36664359..36667558,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267005	TF binding region
ENSG00000105254	Chromatin interaction
ENSG00000105258	Chromatin interaction

Extended variants
information (count: 29 )
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];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10402039	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10402069	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10402367	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10405169	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10409235	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410837	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10420462	0.93[AMR][1000 genomes];0.98[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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1476503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1476504	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1559258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1974843	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4372806	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4630678	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4805162	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]
rs4806282	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249719	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7258520	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103261	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv138090	chr19:36664841-36667019	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6510526	ACTN4	cis	parietal	SCAN
rs6510526	LTBP4	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36642200-36673400	Weak transcription	Primary B cells from cord blood	blood
2	chr19:36643000-36673800	Weak transcription	NH-A	brain
3	chr19:36643800-36673200	Weak transcription	Brain Germinal Matrix	brain
4	chr19:36644400-36673000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:36644400-36673200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:36644400-36673400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr19:36644400-36673400	Weak transcription	Brain Angular Gyrus	brain
8	chr19:36652400-36673400	Weak transcription	Fetal Brain Female	brain
9	chr19:36653000-36673400	Weak transcription	Primary T cells from cord blood	blood
10	chr19:36653200-36673200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:36653200-36673200	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr19:36653200-36673400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:36653200-36673400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr19:36653200-36673400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:36653200-36673400	Weak transcription	HMEC	breast
16	chr19:36653200-36673600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:36653200-36681400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:36653200-36684600	Weak transcription	Aorta	Aorta
19	chr19:36655000-36673600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:36655800-36673400	Weak transcription	Fetal Brain Male	brain
21	chr19:36657800-36673400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:36658000-36673600	Weak transcription	Fetal Stomach	stomach
23	chr19:36660000-36673400	Weak transcription	Lung	lung
24	chr19:36660400-36673400	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr19:36660400-36673400	Weak transcription	HSMMtube	muscle
26	chr19:36660400-36673600	Weak transcription	Pancreas	Pancrea
27	chr19:36660600-36673400	Weak transcription	Thymus	Thymus
28	chr19:36660800-36673200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:36660800-36673200	Weak transcription	HSMM	muscle
30	chr19:36660800-36673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:36660800-36673400	Weak transcription	Brain Substantia Nigra	brain
32	chr19:36660800-36673400	Weak transcription	Esophagus	oesophagus
33	chr19:36660800-36673600	Weak transcription	Right Ventricle	heart
34	chr19:36660800-36673600	Weak transcription	Spleen	Spleen
35	chr19:36661800-36668800	Weak transcription	Psoas Muscle	Psoas
36	chr19:36661800-36673000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:36661800-36673000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr19:36661800-36673000	Weak transcription	Fetal Intestine Small	intestine
39	chr19:36661800-36673200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:36661800-36673200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:36661800-36673200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr19:36661800-36673200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:36661800-36673200	Weak transcription	Adipose Nuclei	Adipose
44	chr19:36661800-36673200	Weak transcription	Liver	Liver
45	chr19:36661800-36673200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:36661800-36673200	Weak transcription	Brain Hippocampus Middle	brain
47	chr19:36661800-36673200	Weak transcription	Colon Smooth Muscle	Colon
48	chr19:36661800-36673200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:36661800-36673200	Weak transcription	Fetal Intestine Large	intestine
50	chr19:36661800-36673200	Weak transcription	Rectal Mucosa Donor 29	rectum

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