Variant report

Variant	rs6752812
Chromosome Location	chr2:172851502-172851503
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	chr2:172844744..172846425-chr2:172851326..172853305,2	K562	blood:
2	chr2:172849902..172852989-chr2:172863264..172866294,5	K562	blood:

Variant related genes	Relation type
ENSG00000172878	Chromatin interaction
ENSG00000115840	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10165126	0.80[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap]
rs10166548	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10174055	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10201430	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10202823	0.91[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12692974	0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs12692978	0.84[CHD][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap]
rs13004237	0.83[AMR][1000 genomes]
rs13017585	0.82[ASW][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap]
rs13030911	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2165934	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35256122	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3770445	0.81[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap]
rs3770451	0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.80[MKK][hapmap]
rs3770452	0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap]
rs4668414	0.91[ASW][hapmap];0.81[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap]
rs6433319	0.92[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6715929	0.88[CEU][hapmap];0.90[TSI][hapmap]
rs6724337	0.81[CHD][hapmap];0.88[GIH][hapmap];0.83[MKK][hapmap]
rs6725388	0.83[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap]
rs6727017	0.88[CEU][hapmap];0.87[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes]
rs6731562	0.91[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs6750058	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6754817	0.91[ASW][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs6758704	0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.82[MKK][hapmap]
rs6759575	0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap]
rs7563971	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7564089	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7573003	0.93[JPT][hapmap]
rs7581072	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586207	0.88[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap]
rs7602037	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs908670	0.88[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.83[MKK][hapmap]
rs908671	0.93[JPT][hapmap]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv821790	chr2:172848378-172854109	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6752812	AC068039.4	cis	Thyroid	GTEx
rs6752812	CYBRD1	cis	multi-tissue	Pritchard
rs6752812	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6752812	AC068039.4	cis	Nerve Tibial	GTEx
rs6752812	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6752812	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6752812	AC068039.4	cis	Stomach	GTEx
rs6752812	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6752812	AC068039.4	cis	Muscle Skeletal	GTEx
rs6752812	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6752812	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6752812	AC068039.4	cis	Whole Blood	GTEx
rs6752812	AC068039.4	cis	lung	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
2	chr2:172796000-172855200	Weak transcription	Gastric	stomach
3	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:172811800-172852200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:172811800-172855600	Weak transcription	Fetal Heart	heart
6	chr2:172813000-172859200	Weak transcription	Fetal Brain Male	brain
7	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:172824000-172857800	Weak transcription	Brain Anterior Caudate	brain
9	chr2:172824000-172857800	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:172840800-172857600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:172843400-172852800	Weak transcription	Aorta	Aorta
12	chr2:172844000-172854000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:172844200-172857200	Weak transcription	Brain Germinal Matrix	brain
14	chr2:172844400-172857400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:172844600-172855600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:172845200-172852000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:172845200-172857600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:172845600-172851600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:172845600-172852200	Weak transcription	GM12878-XiMat	blood
20	chr2:172845600-172854200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:172845600-172854400	Weak transcription	Thymus	Thymus
22	chr2:172845600-172855600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:172846000-172857600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:172846200-172852800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:172847400-172864000	Weak transcription	HSMM	muscle
26	chr2:172847600-172851600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:172847600-172854400	Weak transcription	Fetal Stomach	stomach
28	chr2:172847600-172855000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:172847800-172857600	Weak transcription	Ovary	ovary
30	chr2:172848000-172851600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:172848000-172863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:172848200-172855600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:172848400-172852400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:172848400-172852800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:172848400-172853800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:172848400-172856000	Weak transcription	K562	blood
37	chr2:172848800-172851800	Weak transcription	Fetal Lung	lung
38	chr2:172848800-172855200	Weak transcription	Fetal Intestine Large	intestine
39	chr2:172849000-172851600	Weak transcription	HUVEC	blood vessel
40	chr2:172849000-172852200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:172849000-172853000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:172849000-172854000	Weak transcription	Liver	Liver
43	chr2:172849200-172851600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:172849200-172854200	Weak transcription	Fetal Thymus	thymus
45	chr2:172849200-172855000	Weak transcription	Primary T cells from cord blood	blood
46	chr2:172849200-172856600	Weak transcription	Left Ventricle	heart
47	chr2:172849200-172857200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:172849200-172857400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:172849400-172855400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:172849600-172852200	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links