Variant report

Variant	rs6750058
Chromosome Location	chr2:172786909-172786910
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172769627..172772363-chr2:172785996..172788506,2	K562	blood:
2	chr2:172785586..172787767-chr2:172791438..172793230,2	K562	blood:
3	chr2:172769627..172771187-chr2:172785586..172788506,2	K562	blood:
4	chr2:172779934..172782820-chr2:172786897..172788575,2	MCF-7	breast:
5	chr2:172783996..172786927-chr2:172793285..172795381,2	K562	blood:
6	chr2:172784866..172787052-chr2:172788179..172790740,2	K562	blood:
7	chr2:172785631..172787441-chr2:172963287..172967439,3	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10166548	0.90[AMR][1000 genomes]
rs10174055	0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10201430	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10202823	0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13004237	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13030911	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2165934	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35256122	0.81[AMR][1000 genomes]
rs3770445	0.81[CHB][hapmap]
rs4668414	0.81[CHB][hapmap]
rs62182433	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6433319	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6725388	0.82[CHB][hapmap];0.81[AMR][1000 genomes]
rs6727017	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731562	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752812	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7563971	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7564089	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7573003	0.84[AMR][1000 genomes]
rs7581072	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7602037	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6750058	AC068039.4	cis	Whole Blood	GTEx
rs6750058	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6750058	AC068039.4	cis	lung	GTEx
rs6750058	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6750058	AC068039.4	cis	Thyroid	GTEx
rs6750058	AC068039.4	cis	Esophagus Mucosa	GTEx
rs6750058	AC068039.4	cis	Stomach	GTEx
rs6750058	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6750058	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6750058	AC068039.4	cis	Muscle Skeletal	GTEx
rs6750058	AC068039.4	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172779800-172787200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:172779800-172828400	Weak transcription	Aorta	Aorta
3	chr2:172780000-172789000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:172780000-172791000	Weak transcription	Esophagus	oesophagus
5	chr2:172780000-172812800	Weak transcription	Lung	lung
6	chr2:172780000-172829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:172780200-172787600	Weak transcription	Pancreas	Pancrea
8	chr2:172780200-172789800	Weak transcription	Colonic Mucosa	Colon
9	chr2:172780200-172792800	Weak transcription	Spleen	Spleen
10	chr2:172780200-172795000	Weak transcription	Psoas Muscle	Psoas
11	chr2:172780200-172795400	Weak transcription	Gastric	stomach
12	chr2:172780200-172822200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:172780200-172840400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:172780400-172787000	Weak transcription	Brain Hippocampus Middle	brain
15	chr2:172780400-172787200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:172780400-172796600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:172780400-172820600	Weak transcription	Brain Angular Gyrus	brain
18	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:172780600-172787200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:172780600-172788400	Weak transcription	NH-A	brain
21	chr2:172780600-172795200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:172780600-172811200	Weak transcription	HSMMtube	muscle
23	chr2:172780600-172811200	Weak transcription	NHEK	skin
24	chr2:172780600-172820600	Weak transcription	Brain Anterior Caudate	brain
25	chr2:172780600-172822200	Weak transcription	Liver	Liver
26	chr2:172780600-172822200	Weak transcription	Fetal Kidney	kidney
27	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
29	chr2:172781000-172787600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:172781000-172789800	Weak transcription	NHLF	lung
31	chr2:172781000-172792600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:172781000-172795400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:172781000-172811000	Weak transcription	Right Ventricle	heart
34	chr2:172781000-172811200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:172781200-172788000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr2:172781200-172801400	Weak transcription	NHDF-Ad	bronchial
37	chr2:172781200-172808800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:172781200-172811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:172781400-172788200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:172781400-172788200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr2:172781400-172792400	Weak transcription	Fetal Heart	heart
42	chr2:172781400-172822000	Weak transcription	HUVEC	blood vessel
43	chr2:172781800-172788400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:172781800-172790000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:172782000-172787600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:172782000-172788000	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr2:172782200-172789800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:172782400-172788800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:172782600-172788800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:172782600-172789000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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