Variant report

Variant	rs2069274
Chromosome Location	chr4:104020781-104020782
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103997335..103999148-chr4:104019345..104021953,2	K562	blood:
2	chr4:103997337..103998985-chr4:104019484..104022200,2	K562	blood:

Variant related genes	Relation type
ENSG00000164038	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1031804	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727498	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12501621	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17217473	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2045746	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2126470	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169508	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2251322	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251634	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2615539	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623060	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2623064	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623070	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2711897	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2711898	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711899	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720448	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720458	0.96[CEU][hapmap];0.88[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720460	0.96[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720461	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720462	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720464	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2720468	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720469	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720471	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866635	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699050	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699051	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533056	0.92[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6810571	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6813563	0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6815783	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6841136	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6850461	0.92[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2069274	PPP3CA	cis	parietal	SCAN
rs2069274	MANBA	cis	multi-tissue	Pritchard
rs2069274	BDH2	cis	Thyroid	GTEx
rs2069274	BDH2	cis	cerebellum	SCAN
rs2069274	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2069274	BDH2	cis	Muscle Skeletal	GTEx
rs2069274	BDH2	cis	lung	GTEx
rs2069274	BDH2	cis	Esophagus Muscularis	GTEx
rs2069274	KRT8P46	cis	lung	GTEx
rs2069274	BDH2	cis	Artery Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104012400-104028200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:104019400-104020800	Flanking Active TSS	Osteobl	bone
3	chr4:104019400-104021200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr4:104019600-104020800	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr4:104019600-104020800	Flanking Active TSS	Brain Cingulate Gyrus	brain
6	chr4:104019800-104020800	Flanking Active TSS	Liver	Liver
7	chr4:104019800-104020800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
8	chr4:104019800-104020800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr4:104019800-104021000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:104019800-104021000	Active TSS	Fetal Stomach	stomach
11	chr4:104019800-104021200	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr4:104019800-104021200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:104019800-104030200	Weak transcription	Esophagus	oesophagus
14	chr4:104020000-104020800	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr4:104020000-104020800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr4:104020000-104020800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr4:104020000-104020800	Flanking Active TSS	HUVEC	blood vessel
18	chr4:104020000-104020800	Flanking Active TSS	NHEK	skin
19	chr4:104020000-104021000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:104020000-104021000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:104020000-104021000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr4:104020000-104021000	Active TSS	Brain Angular Gyrus	brain
23	chr4:104020000-104021000	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr4:104020000-104021000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr4:104020000-104021000	Active TSS	Right Atrium	heart
26	chr4:104020000-104021000	Active TSS	Right Ventricle	heart
27	chr4:104020000-104021000	Active TSS	NHLF	lung
28	chr4:104020000-104021200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:104020000-104021200	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr4:104020000-104021200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:104020000-104021200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr4:104020000-104021200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:104020000-104021200	Active TSS	Fetal Intestine Large	intestine
34	chr4:104020000-104021200	Active TSS	Fetal Intestine Small	intestine
35	chr4:104020000-104021200	Active TSS	Fetal Muscle Trunk	muscle
36	chr4:104020000-104021200	Active TSS	Ovary	ovary
37	chr4:104020000-104021200	Active TSS	HSMMtube	muscle
38	chr4:104020000-104021400	Active TSS	Stomach Smooth Muscle	stomach
39	chr4:104020000-104026400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:104020200-104020800	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr4:104020200-104020800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr4:104020200-104020800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr4:104020200-104020800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr4:104020200-104021000	Active TSS	ES-I3 Cell Line	embryonic stem cell
45	chr4:104020200-104021000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:104020200-104021000	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr4:104020200-104021000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr4:104020200-104021000	Active TSS	Aorta	Aorta
49	chr4:104020200-104021000	Active TSS	Brain Germinal Matrix	brain
50	chr4:104020200-104021000	ZNF genes & repeats	Fetal Brain Male	brain

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