Variant report

Variant	rs3820640
Chromosome Location	chr1:226868918-226868919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:226861295..226863983-chr1:226866100..226869363,3	K562	blood:
2	chr1:226864917..226866884-chr1:226868100..226871098,3	K562	blood:
3	chr1:226857711..226860069-chr1:226867433..226869238,2	K562	blood:
4	chr1:226864917..226867492-chr1:226868629..226873346,4	K562	blood:

Variant related genes	Relation type
ENSG00000228382	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1070361	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1071530	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288936	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1288938	0.87[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1288939	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17589895	1.00[YRI][hapmap]
rs3768393	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs3768396	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41440951	1.00[YRI][hapmap]
rs697847	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs708766	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3820640	PARP1	cis	cerebellum	SCAN
rs3820640	HIST3H2BB	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226864200-226871600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:226865600-226878000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:226866200-226870600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:226866400-226874800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:226866800-226874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:226867000-226869200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:226867000-226871800	Weak transcription	Dnd41	blood
8	chr1:226867600-226870000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:226867800-226869000	Enhancers	Fetal Heart	heart
10	chr1:226867800-226874200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:226868000-226869000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:226868000-226869400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:226868000-226870000	Weak transcription	Esophagus	oesophagus
14	chr1:226868000-226876000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:226868200-226869000	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
16	chr1:226868200-226869000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:226868200-226869000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:226868200-226869000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:226868200-226869000	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr1:226868200-226869400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:226868200-226869400	Enhancers	Right Ventricle	heart
22	chr1:226868200-226870000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:226868200-226870000	Enhancers	Primary T cells fromperipheralblood	blood
24	chr1:226868200-226870200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:226868200-226870400	Enhancers	Fetal Stomach	stomach
26	chr1:226868200-226870600	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr1:226868200-226870800	Weak transcription	Gastric	stomach
28	chr1:226868200-226871000	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:226868200-226871000	Enhancers	Placenta	Placenta
30	chr1:226868200-226871000	Enhancers	Lung	lung
31	chr1:226868200-226871600	Enhancers	Brain Cingulate Gyrus	brain
32	chr1:226868200-226872000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:226868200-226873400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:226868200-226877400	Enhancers	Left Ventricle	heart
35	chr1:226868200-226884600	Enhancers	Brain Substantia Nigra	brain
36	chr1:226868400-226869000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:226868400-226869000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr1:226868400-226869000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:226868400-226869000	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:226868400-226869000	Enhancers	Fetal Intestine Small	intestine
41	chr1:226868400-226869000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr1:226868400-226869200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr1:226868400-226869200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
44	chr1:226868400-226869200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:226868400-226869200	Enhancers	Fetal Muscle Trunk	muscle
46	chr1:226868400-226870000	Enhancers	Fetal Brain Female	brain
47	chr1:226868400-226870400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:226868400-226870600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:226868400-226870800	Enhancers	Right Atrium	heart
50	chr1:226868400-226872000	Genic enhancers	Primary T cells from cord blood	blood

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