Variant report

Variant	rs12501621
Chromosome Location	chr4:104095505-104095506
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:104094045..104096385-chr4:104103040..104105697,2	K562	blood:
2	chr4:104094724..104096595-chr4:104098103..104100589,2	K562	blood:

Variant related genes	Relation type
ENSG00000138778	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1031804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11727498	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17217473	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045746	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2069274	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]
rs2126470	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169508	0.94[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2251322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2251634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2615539	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2623060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2623064	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]
rs2623070	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2711897	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2711898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2711899	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2720448	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720458	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720460	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720461	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2720462	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2720464	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2720468	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2720469	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2720471	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2866635	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699050	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4699051	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6533056	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6810571	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6813563	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]
rs6815783	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6822891	0.83[YRI][hapmap]
rs6841136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6850461	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7656438	0.84[AMR][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12501621	KRT8P46	cis	lung	GTEx
rs12501621	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs12501621	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs12501621	BDH2	cis	Thyroid	GTEx
rs12501621	BDH2	cis	Skin Sun Exposed Lower leg	GTEx
rs12501621	BDH2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:78 , 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	chr4:104038200-104095800	Strong transcription	Fetal Thymus	thymus
3	chr4:104058200-104118400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:104065000-104113200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr4:104073600-104118400	Weak transcription	Fetal Kidney	kidney
6	chr4:104078400-104108400	Strong transcription	Dnd41	blood
7	chr4:104080000-104101800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:104088600-104109000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:104089800-104098800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:104089800-104114800	Weak transcription	Placenta	Placenta
11	chr4:104089800-104118200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:104089800-104119000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr4:104090000-104097600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:104090000-104098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr4:104090000-104118000	Weak transcription	Fetal Stomach	stomach
16	chr4:104090000-104118600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:104090000-104119000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:104090200-104098400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:104090200-104098400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:104090200-104098400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr4:104090200-104098400	Weak transcription	Thymus	Thymus
22	chr4:104090200-104098400	Weak transcription	HepG2	liver
23	chr4:104090200-104098600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr4:104090200-104100000	Weak transcription	NHEK	skin
25	chr4:104090200-104100200	Weak transcription	NHLF	lung
26	chr4:104090200-104107400	Weak transcription	Primary B cells from cord blood	blood
27	chr4:104090200-104118200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr4:104090200-104118200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:104090200-104118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:104090200-104118200	Weak transcription	Fetal Intestine Small	intestine
31	chr4:104090400-104118200	Weak transcription	Fetal Brain Male	brain
32	chr4:104090600-104107000	Weak transcription	Hela-S3	cervix
33	chr4:104090600-104109600	Weak transcription	Primary T cells from cord blood	blood
34	chr4:104090600-104117600	Weak transcription	Fetal Heart	heart
35	chr4:104090800-104097000	Weak transcription	A549	lung
36	chr4:104090800-104097800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:104090800-104098000	Weak transcription	NH-A	brain
38	chr4:104090800-104098200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:104090800-104098400	Weak transcription	Fetal Muscle Leg	muscle
40	chr4:104090800-104098600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:104090800-104098600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr4:104090800-104100400	Weak transcription	Brain Germinal Matrix	brain
43	chr4:104090800-104100400	Weak transcription	Fetal Lung	lung
44	chr4:104090800-104102400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:104090800-104118200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr4:104091000-104098800	Weak transcription	Fetal Brain Female	brain
47	chr4:104091000-104100200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:104091200-104097600	Strong transcription	NHDF-Ad	bronchial
49	chr4:104091600-104108400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:104091800-104097800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links