Variant report

Variant	rs3826995
Chromosome Location	chr19:36581636-36581637
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36580223..36582667-chr19:36584445..36586410,2	MCF-7	breast:
2	chr19:36580161..36582596-chr19:36590218..36593086,2	MCF-7	breast:
3	chr19:36498602..36503507-chr19:36579636..36582472,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181392	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1003470	0.87[YRI][hapmap]
rs10407011	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10414877	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10420353	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10421966	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10423651	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10425692	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426582	0.85[CHB][hapmap]
rs12462432	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12462632	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12462674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12972490	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12976505	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12976812	0.90[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12977802	0.84[JPT][hapmap]
rs12977814	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978482	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12981654	0.92[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1548505	0.87[YRI][hapmap]
rs17639286	0.92[CEU][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs2023865	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2072606	0.89[JPT][hapmap]
rs2239510	0.96[CEU][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2301736	0.87[YRI][hapmap]
rs2311004	0.83[YRI][hapmap]
rs35125548	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35875194	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4461192	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4805154	0.85[CHB][hapmap]
rs4806280	0.84[JPT][hapmap]
rs56034793	0.87[ASN][1000 genomes]
rs62109743	0.87[ASN][1000 genomes]
rs71337524	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs721542	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7245762	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7246292	0.87[YRI][hapmap]
rs7250448	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs7257383	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7259592	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7260609	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8103569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[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	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3826995	CYP2B7P1	cis	parietal	SCAN
rs3826995	GRIK5	cis	cerebellum	SCAN
rs3826995	PSG9	cis	cerebellum	SCAN
rs3826995	CCDC97	cis	parietal	SCAN
rs3826995	ZNF229	cis	parietal	SCAN
rs3826995	ZNF345	cis	parietal	SCAN
rs3826995	SHKBP1	cis	cerebellum	SCAN
rs3826995	THAP8	cis	multi-tissue	Pritchard
rs3826995	ATXN7L1	trans	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
2	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
3	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
8	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
10	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
11	chr19:36561200-36587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:36561200-36597600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:36561200-36597600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:36561200-36597600	Strong transcription	Dnd41	blood
15	chr19:36561200-36598200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr19:36561200-36598400	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr19:36561400-36587800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:36561400-36596400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr19:36561400-36596600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr19:36562000-36588600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr19:36562200-36585000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:36563000-36594200	Weak transcription	HSMM	muscle
23	chr19:36564800-36584600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:36566000-36592000	Weak transcription	HMEC	breast
25	chr19:36568600-36598000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr19:36568800-36594800	Strong transcription	A549	lung
27	chr19:36568800-36601400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:36570000-36598000	Strong transcription	Fetal Thymus	thymus
29	chr19:36570200-36585200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:36571200-36583800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr19:36571600-36584600	Strong transcription	Thymus	Thymus
32	chr19:36571600-36586400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr19:36571600-36596600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr19:36571800-36588400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr19:36571800-36588600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:36571800-36591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:36571800-36598400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:36571800-36600000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:36571800-36600600	Strong transcription	Fetal Stomach	stomach
40	chr19:36572000-36598000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr19:36572200-36585400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr19:36572200-36586400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:36572200-36586600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:36572200-36588200	Strong transcription	Fetal Muscle Leg	muscle
45	chr19:36572400-36585800	Strong transcription	Fetal Intestine Small	intestine
46	chr19:36572400-36588400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr19:36572400-36588400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr19:36572400-36602400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr19:36572800-36583800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:36572800-36586000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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