Variant report

Variant	rs6813563
Chromosome Location	chr4:104099110-104099111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104094724..104096595-chr4:104098103..104100589,2	K562	blood:
2	chr4:104098535..104101174-chr4:104177229..104179251,2	K562	blood:

Variant related genes	Relation type
ENSG00000248740	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1031804	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11727498	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12501621	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17217473	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2045746	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2069274	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]
rs2126470	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2169508	0.94[CHB][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2251322	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251634	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2615539	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2623060	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2623064	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]
rs2623070	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2711897	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2711898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2711899	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720448	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2720458	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2720460	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2720461	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2720462	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2720464	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720468	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2720469	0.84[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720471	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2866635	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4699050	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699051	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6533056	0.83[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6810571	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6815783	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6841136	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6850461	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7656438	0.84[AMR][1000 genomes];0.81[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	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
2	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
3	nsv1015023	chr4:104039145-104565217	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv830022	chr4:104087199-104257784	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6813563	BDH2	cis	Thyroid	GTEx
rs6813563	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs6813563	BDH2	cis	Artery Tibial	GTEx
rs6813563	BDH2	cis	Adipose Subcutaneous	GTEx
rs6813563	BDH2	cis	cerebellum	SCAN
rs6813563	PPP3CA	cis	parietal	SCAN
rs6813563	BDH2	cis	Muscle Skeletal	GTEx
rs6813563	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs6813563	BDH2	cis	parietal	SCAN
rs6813563	KRT8P46	cis	lung	GTEx
rs6813563	BDH2	cis	Esophagus Muscularis	GTEx
rs6813563	MANBA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:104021200-104100200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:104065000-104113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr4:104073600-104118400	Weak transcription	Fetal Kidney	kidney
5	chr4:104078400-104108400	Strong transcription	Dnd41	blood
6	chr4:104080000-104101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:104088600-104109000	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr4:104089800-104114800	Weak transcription	Placenta	Placenta
9	chr4:104089800-104118200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:104089800-104119000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:104090000-104118000	Weak transcription	Fetal Stomach	stomach
12	chr4:104090000-104118600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr4:104090000-104119000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:104090200-104100000	Weak transcription	NHEK	skin
15	chr4:104090200-104100200	Weak transcription	NHLF	lung
16	chr4:104090200-104107400	Weak transcription	Primary B cells from cord blood	blood
17	chr4:104090200-104118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:104090200-104118200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:104090200-104118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:104090200-104118200	Weak transcription	Fetal Intestine Small	intestine
21	chr4:104090400-104118200	Weak transcription	Fetal Brain Male	brain
22	chr4:104090600-104107000	Weak transcription	Hela-S3	cervix
23	chr4:104090600-104109600	Weak transcription	Primary T cells from cord blood	blood
24	chr4:104090600-104117600	Weak transcription	Fetal Heart	heart
25	chr4:104090800-104100400	Weak transcription	Brain Germinal Matrix	brain
26	chr4:104090800-104100400	Weak transcription	Fetal Lung	lung
27	chr4:104090800-104102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:104090800-104118200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr4:104091000-104100200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:104091600-104108400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:104092000-104108400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:104092800-104099400	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:104093600-104108400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:104093600-104108400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:104094000-104108200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:104094000-104108400	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:104094200-104108200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:104094400-104108200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr4:104094600-104108400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:104094800-104108200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:104095200-104099200	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr4:104095200-104118800	Weak transcription	Adipose Nuclei	Adipose
43	chr4:104096600-104108400	Strong transcription	Fetal Thymus	thymus
44	chr4:104096600-104108400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:104096800-104102000	Strong transcription	HSMM	muscle
46	chr4:104096800-104105400	Strong transcription	Osteobl	bone
47	chr4:104097000-104100400	Weak transcription	GM12878-XiMat	blood
48	chr4:104097000-104119000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr4:104097400-104100000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:104097600-104100200	Weak transcription	NHDF-Ad	bronchial

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