Variant report

Variant	rs828889
Chromosome Location	chr2:74371995-74371996
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	POLR2A	chr2:74371921-74372633	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
2	chr2:74367938..74377304-chr2:74421816..74428438,25	K562	blood:
3	chr2:74345450..74348977-chr2:74371413..74376785,7	MCF-7	breast:

Variant related genes	Relation type
BOLA3-AS1	TF binding region
ENSG00000065911	Chromatin interaction
ENSG00000257800	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11126426	0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1620482	0.96[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667601	0.88[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1667605	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1667606	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667609	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1723292	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34611905	0.83[EUR][1000 genomes]
rs35864597	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546893	0.82[ASN][1000 genomes]
rs702462	0.87[GIH][hapmap]
rs702466	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7340453	0.87[GIH][hapmap]
rs7559252	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7562297	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828856	0.87[ASN][1000 genomes]
rs828873	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828876	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs828877	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828882	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828883	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs828884	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828885	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828886	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828888	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828903	0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs844168	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv525117	chr2:74358901-74374641	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs828889	NAT8	cis	parietal	SCAN
rs828889	MTHFD2	cis	multi-tissue	Pritchard
rs828889	MTHFD2	cis	lymphoblastoid	seeQTL
rs828889	ALMS1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74354400-74373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:74355200-74373800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:74357600-74373800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:74357800-74373600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:74358200-74373800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr2:74358800-74373800	Weak transcription	HUVEC	blood vessel
7	chr2:74359200-74373600	Weak transcription	Fetal Heart	heart
8	chr2:74359400-74373600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:74359600-74373400	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:74359600-74373800	Weak transcription	Small Intestine	intestine
11	chr2:74359800-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:74359800-74373600	Weak transcription	NH-A	brain
13	chr2:74360200-74373600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:74360600-74373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:74360800-74373600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:74360800-74373800	Weak transcription	Placenta	Placenta
17	chr2:74360800-74374000	Weak transcription	HSMMtube	muscle
18	chr2:74362000-74373600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:74362200-74373400	Weak transcription	Fetal Lung	lung
20	chr2:74362200-74373600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:74362200-74373600	Weak transcription	HMEC	breast
22	chr2:74362200-74374000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:74362200-74374600	Weak transcription	Aorta	Aorta
24	chr2:74362400-74373400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:74362400-74373400	Weak transcription	Right Ventricle	heart
26	chr2:74362400-74373600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:74362400-74373600	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:74362400-74373600	Weak transcription	Brain Angular Gyrus	brain
29	chr2:74362400-74373600	Weak transcription	Psoas Muscle	Psoas
30	chr2:74362400-74373800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:74362600-74373400	Weak transcription	Hela-S3	cervix
32	chr2:74362800-74373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:74362800-74373600	Weak transcription	Liver	Liver
34	chr2:74364200-74373600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:74364400-74372400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:74364800-74372000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr2:74365000-74373400	Strong transcription	Fetal Stomach	stomach
38	chr2:74365200-74372200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:74365200-74372200	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:74365200-74372400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:74365200-74373400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:74365400-74372200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:74365800-74372200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:74365800-74373800	Weak transcription	Ovary	ovary
45	chr2:74366000-74372400	Strong transcription	Fetal Intestine Small	intestine
46	chr2:74366000-74372600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:74366200-74373400	Weak transcription	Fetal Kidney	kidney
48	chr2:74366400-74372400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:74366600-74374200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:74366800-74372400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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