Variant report

Variant	rs3810383
Chromosome Location	chr19:40315402-40315403
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39900714..39902326-chr19:40314340..40316336,2	MCF-7	breast:
2	chr19:40314923..40317084-chr19:40321250..40326069,8	MCF-7	breast:
3	chr19:40305000..40306597-chr19:40314975..40317382,2	K562	blood:
4	chr19:40301803..40305513-chr19:40314560..40316955,3	MCF-7	breast:
5	chr19:40296262..40298626-chr19:40313380..40316915,4	MCF-7	breast:
6	chr19:40313245..40319369-chr19:40333328..40340168,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105204	Chromatin interaction
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10422280	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[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];1.00[ASN][1000 genomes]
rs11880094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11883249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12459589	0.81[GIH][hapmap]
rs12975624	0.86[CHB][hapmap];0.88[GIH][hapmap];0.86[MEX][hapmap]
rs12980289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[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];1.00[ASN][1000 genomes]
rs12986299	0.84[CHB][hapmap]
rs2072290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354471	0.81[GIH][hapmap]
rs2354800	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810386	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs616650	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62106867	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508912	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508913	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718066	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246501	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7247063	0.81[GIH][hapmap]
rs7248926	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250408	0.82[GIH][hapmap]
rs7253739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254914	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3810383	B9D2	cis	cerebellum	SCAN
rs3810383	PHLDB3	cis	parietal	SCAN
rs3810383	ERF	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40312000-40323200	Strong transcription	A549	lung
2	chr19:40312200-40316800	Weak transcription	Hela-S3	cervix
3	chr19:40313600-40320200	Weak transcription	K562	blood
4	chr19:40314200-40315600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr19:40314200-40315600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:40314200-40315600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr19:40314200-40315600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr19:40314200-40315600	Active TSS	Fetal Kidney	kidney
9	chr19:40314200-40315600	Active TSS	NHDF-Ad	bronchial
10	chr19:40314200-40315800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:40314200-40315800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr19:40314200-40315800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:40314200-40315800	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr19:40314200-40316000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr19:40314400-40315600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr19:40314400-40315600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr19:40314400-40315800	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr19:40314400-40315800	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:40314400-40315800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:40314400-40315800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr19:40314400-40315800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr19:40314400-40315800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:40314600-40315600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr19:40314600-40315600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:40314600-40315600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:40314600-40315600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:40314600-40315600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr19:40314600-40315600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:40314600-40315600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:40314600-40315600	Active TSS	Right Atrium	heart
31	chr19:40314600-40315600	Active TSS	Right Ventricle	heart
32	chr19:40314600-40315600	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr19:40314600-40315600	Active TSS	NHEK	skin
34	chr19:40314600-40316000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr19:40314600-40316000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:40314800-40315600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:40314800-40315600	Active TSS	Rectal Smooth Muscle	rectum
38	chr19:40315000-40315600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr19:40315000-40315600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:40315000-40315600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:40315000-40315600	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:40315000-40315600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:40315000-40315600	Active TSS	Brain Germinal Matrix	brain
44	chr19:40315000-40315600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr19:40315000-40315600	Active TSS	Colonic Mucosa	Colon
46	chr19:40315000-40315600	Active TSS	Duodenum Mucosa	Duodenum
47	chr19:40315000-40315600	Active TSS	Thymus	Thymus
48	chr19:40315200-40315600	Active TSS	Primary T cells from cord blood	blood
49	chr19:40315200-40315600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:40315200-40315600	Active TSS	Stomach Smooth Muscle	stomach

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