Variant report

Variant	rs2623064
Chromosome Location	chr4:104030792-104030793
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104030107..104032636-chr4:104037443..104039325,2	K562	blood:
2	chr4:104022090..104023691-chr4:104028636..104031438,2	K562	blood:

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

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

rs_ID	r²[population]
rs1031804	0.92[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12501621	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17217473	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045746	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069274	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]
rs2126470	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169508	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2251322	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2251634	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2615539	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623060	0.96[CEU][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2623070	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2711897	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2711898	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711899	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2720448	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720458	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720460	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720461	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720462	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720464	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720468	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720469	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720471	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2866635	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699050	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4699051	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533056	0.88[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6810571	0.96[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6813563	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6815783	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841136	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6850461	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.86[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
rs2623064	BDH2	cis	lung	GTEx
rs2623064	BDH2	cis	Esophagus Muscularis	GTEx
rs2623064	PPP3CA	cis	parietal	SCAN
rs2623064	BDH2	cis	Thyroid	GTEx
rs2623064	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs2623064	BDH2	cis	Artery Tibial	GTEx
rs2623064	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs2623064	KRT8P46	cis	lung	GTEx
rs2623064	BDH2	cis	cerebellum	SCAN
rs2623064	BDH2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021000-104031600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:104021000-104031600	Weak transcription	Placenta	Placenta
3	chr4:104021000-104033600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:104021000-104049200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr4:104021000-104049200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:104021000-104056000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:104021000-104058200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr4:104021000-104063800	Weak transcription	Fetal Stomach	stomach
9	chr4:104021000-104068400	Weak transcription	Fetal Brain Male	brain
10	chr4:104021000-104076400	Weak transcription	Fetal Brain Female	brain
11	chr4:104021000-104089600	Weak transcription	Fetal Heart	heart
12	chr4:104021200-104032400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:104021200-104032600	Weak transcription	Fetal Kidney	kidney
14	chr4:104021200-104032800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:104021200-104045800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:104021200-104076600	Weak transcription	Fetal Intestine Small	intestine
17	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:104021400-104030800	Weak transcription	A549	lung
19	chr4:104021400-104074600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr4:104026200-104031600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:104026200-104033200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:104026200-104033400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:104026400-104033000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr4:104026600-104033200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr4:104026800-104046200	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:104027000-104033200	Strong transcription	Fetal Thymus	thymus
27	chr4:104027200-104031200	Strong transcription	Thymus	Thymus
28	chr4:104027200-104032400	Strong transcription	GM12878-XiMat	blood
29	chr4:104027200-104032600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr4:104027200-104032600	Strong transcription	Fetal Muscle Leg	muscle
31	chr4:104027200-104033000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:104027200-104033200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:104027200-104033200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:104027200-104033200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:104027200-104033200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:104027200-104033200	Strong transcription	HMEC	breast
37	chr4:104027200-104033400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:104027200-104033400	Strong transcription	Dnd41	blood
39	chr4:104027200-104033800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:104027600-104031000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr4:104027600-104033000	Strong transcription	HUVEC	blood vessel
42	chr4:104027600-104038400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:104027800-104033200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:104028000-104030800	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:104028000-104032000	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr4:104028000-104032600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:104028000-104033200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:104028200-104031200	Strong transcription	Primary B cells from cord blood	blood
49	chr4:104028200-104033200	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr4:104028400-104032600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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