Variant report

Variant	rs3764567
Chromosome Location	chr19:19440066-19440067
allele	C/T
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	SPI1	chr19:19439847-19440445	HL-60	blood:	n/a	chr19:19440202-19440209 chr19:19440227-19440236
2	POLR2A	chr19:19439929-19440149	K562	blood:	n/a	n/a
3	POLR2A	chr19:19439992-19440335	HUVEC	blood vessel:	n/a	n/a
4	MYC	chr19:19440026-19440134	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:19439973-19440152	HUVEC	blood vessel:	n/a	n/a
6	FOS	chr19:19439897-19440341	HUVEC	blood vessel:	n/a	chr19:19440130-19440138 chr19:19440128-19440139
7	POLR2A	chr19:19439954-19440091	HepG2	liver:	n/a	n/a
8	POLR2A	chr19:19439587-19440168	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19439707..19441657-chr19:19442006..19443509,2	MCF-7	breast:
2	chr19:19301973..19304677-chr19:19438617..19440133,2	MCF-7	breast:
3	chr19:19435098..19437223-chr19:19438323..19441440,3	K562	blood:
4	chr19:19436638..19438572-chr19:19438797..19440377,2	MCF-7	breast:
5	chr19:19438751..19440624-chr19:19603329..19605522,2	K562	blood:
6	chr19:19429265..19433955-chr19:19435114..19441517,10	K562	blood:
7	chr19:19433505..19435144-chr19:19437527..19440100,2	MCF-7	breast:

Variant related genes	Relation type
MAU2	TF binding region
ENSG00000254901	Chromatin interaction
ENSG00000213999	Chromatin interaction
ENSG00000105705	Chromatin interaction
ENSG00000129933	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000064489	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1000237	0.88[CEU][hapmap]
rs1009136	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs1010207	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs10282	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs10401193	0.84[JPT][hapmap]
rs10414830	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs10419912	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs1054284	0.92[CEU][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs1063966	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs11085259	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11669516	0.80[JPT][hapmap]
rs12972397	0.84[JPT][hapmap]
rs12973258	0.84[JPT][hapmap]
rs12977524	0.84[JPT][hapmap]
rs13964	0.96[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs1469712	0.96[CEU][hapmap]
rs1469713	0.88[CEU][hapmap]
rs15622	0.96[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs1858999	0.88[CEU][hapmap]
rs1859287	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2023883	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2074089	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2074090	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap]
rs2074296	0.88[CHB][hapmap];0.91[CHD][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2074301	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs2074303	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2074550	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2163804	0.84[JPT][hapmap]
rs2269873	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2285627	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2285628	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2288852	0.92[CEU][hapmap]
rs2301668	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs2301784	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2301786	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2315025	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2315610	0.92[CEU][hapmap]
rs2905421	0.92[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs2905424	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs2905425	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs2916074	0.88[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs2916076	0.87[CEU][hapmap]
rs2965180	0.96[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2965183	0.87[CEU][hapmap]
rs2965185	0.81[CEU][hapmap]
rs2965188	0.96[CEU][hapmap]
rs2965189	0.88[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs2965193	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs2965198	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs34277109	0.96[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs3752151	0.92[CEU][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs3794990	0.92[CEU][hapmap]
rs3794993	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4808199	0.84[JPT][hapmap]
rs4808200	0.96[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4808203	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs4808957	0.92[CEU][hapmap]
rs4808959	0.92[CEU][hapmap]
rs4808960	0.84[JPT][hapmap]
rs4808961	0.88[CEU][hapmap]
rs4808964	0.92[CEU][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs4808965	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs6511026	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs6511036	0.84[JPT][hapmap]
rs6909	0.92[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs7252888	0.84[JPT][hapmap]
rs7254230	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7254748	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs7259434	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs735273	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs747050	0.92[CEU][hapmap]
rs769267	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs8103197	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap]
rs8103496	0.88[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap]
rs8105094	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs8105984	0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs8108647	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs892021	0.87[CEU][hapmap]
rs892022	0.92[CEU][hapmap];0.84[JPT][hapmap]
rs968525	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3764567	TM6SF2	cis	cerebellum	SCAN
rs3764567	HAUS8	cis	parietal	SCAN
rs3764567	GATAD2A	cis	parietal	SCAN
rs3764567	KIAA0892	cis	multi-tissue	Pritchard
rs3764567	ZNF826P	cis	parietal	SCAN
rs3764567	IL12RB1	cis	parietal	SCAN
rs3764567	DDX49	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19432600-19445400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:19432800-19445400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:19432800-19447400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:19433200-19452800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:19433400-19440200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:19433400-19469800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:19433400-19470600	Strong transcription	Fetal Stomach	stomach
8	chr19:19433600-19448800	Weak transcription	Stomach Mucosa	stomach
9	chr19:19433800-19468400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:19433800-19469800	Strong transcription	Fetal Intestine Large	intestine
11	chr19:19433800-19470400	Strong transcription	Placenta	Placenta
12	chr19:19434000-19445600	Strong transcription	Fetal Intestine Small	intestine
13	chr19:19434200-19469000	Strong transcription	Fetal Thymus	thymus
14	chr19:19434200-19469800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:19434200-19469800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr19:19434400-19443600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:19434400-19449800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:19434400-19450600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr19:19434600-19445400	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr19:19434600-19448200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:19434600-19466000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr19:19434800-19448000	Weak transcription	Psoas Muscle	Psoas
23	chr19:19434800-19470600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:19435000-19471000	Strong transcription	Fetal Brain Female	brain
25	chr19:19435200-19448200	Strong transcription	Osteobl	bone
26	chr19:19435200-19449200	Weak transcription	Fetal Brain Male	brain
27	chr19:19435400-19444200	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:19435400-19444400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:19435400-19453400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr19:19435600-19444000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr19:19435600-19455400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr19:19435600-19468600	Strong transcription	Dnd41	blood
33	chr19:19435600-19470400	Strong transcription	Brain Germinal Matrix	brain
34	chr19:19435600-19477600	Weak transcription	Fetal Heart	heart
35	chr19:19436000-19444200	Strong transcription	Fetal Muscle Leg	muscle
36	chr19:19436000-19447400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr19:19436000-19460600	Strong transcription	Brain Cingulate Gyrus	brain
38	chr19:19436400-19441600	Weak transcription	Colonic Mucosa	Colon
39	chr19:19436800-19445200	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr19:19436800-19455600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:19437000-19442400	Weak transcription	HSMM	muscle
42	chr19:19437000-19449000	Weak transcription	Fetal Kidney	kidney
43	chr19:19437200-19444200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:19438200-19444600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:19438200-19444800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:19438200-19448600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:19438200-19450000	Strong transcription	Primary T cells from cord blood	blood
48	chr19:19438200-19469600	Strong transcription	Thymus	Thymus
49	chr19:19438400-19440400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr19:19438400-19440400	Strong transcription	A549	lung

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