Variant report

Variant	rs2165934
Chromosome Location	chr2:172812339-172812340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172807381..172810249-chr2:172812203..172814108,2	K562	blood:
2	chr2:172811747..172815562-chr2:172948596..172951136,4	MCF-7	breast:
3	chr2:172807954..172811723-chr2:172812087..172815837,4	K562	blood:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10165126	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174055	0.83[AMR][1000 genomes]
rs10201430	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10202823	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13004237	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13030911	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62182433	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433319	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6727017	0.83[EUR][1000 genomes]
rs6731562	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6750058	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6752812	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7563971	0.85[EUR][1000 genomes]
rs7564089	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7581072	0.83[AMR][1000 genomes]
rs7602037	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2165934	AC068039.4	cis	Heart Left Ventricle	GTEx
rs2165934	AC068039.4	cis	Esophagus Mucosa	GTEx
rs2165934	AC068039.4	cis	Thyroid	GTEx
rs2165934	AC068039.4	cis	Muscle Skeletal	GTEx
rs2165934	AC068039.4	cis	Whole Blood	GTEx
rs2165934	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs2165934	SLC25A12	cis	Whole Blood	GTEx
rs2165934	AC068039.4	cis	Stomach	GTEx
rs2165934	AC068039.4	cis	Nerve Tibial	GTEx
rs2165934	AC068039.4	cis	Esophagus Muscularis	GTEx
rs2165934	AC068039.4	cis	lung	GTEx
rs2165934	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2165934	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172779800-172828400	Weak transcription	Aorta	Aorta
2	chr2:172780000-172812800	Weak transcription	Lung	lung
3	chr2:172780000-172829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:172780200-172822200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:172780200-172840400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:172780400-172820600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:172780600-172820600	Weak transcription	Brain Anterior Caudate	brain
9	chr2:172780600-172822200	Weak transcription	Liver	Liver
10	chr2:172780600-172822200	Weak transcription	Fetal Kidney	kidney
11	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
13	chr2:172781400-172822000	Weak transcription	HUVEC	blood vessel
14	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:172784600-172815000	Weak transcription	Left Ventricle	heart
16	chr2:172785400-172822200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:172785400-172822400	Weak transcription	Placenta	Placenta
18	chr2:172785800-172822200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr2:172787200-172812800	Weak transcription	Fetal Brain Male	brain
20	chr2:172787800-172822200	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:172788000-172812600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:172788400-172812800	Weak transcription	Pancreas	Pancrea
23	chr2:172790400-172825200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr2:172793000-172817200	Weak transcription	Right Atrium	heart
25	chr2:172796000-172855200	Weak transcription	Gastric	stomach
26	chr2:172796800-172820600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:172796800-172832200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:172797000-172822200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:172797000-172822200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:172798200-172812400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:172798200-172822200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:172798200-172822600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:172798400-172820600	Weak transcription	Brain Germinal Matrix	brain
34	chr2:172805000-172822200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr2:172805400-172822000	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:172805600-172812800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:172806400-172822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:172807400-172845400	Weak transcription	Spleen	Spleen
39	chr2:172807600-172822400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr2:172808000-172847200	Weak transcription	Fetal Brain Female	brain
41	chr2:172808000-172849400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:172808200-172814200	Strong transcription	Dnd41	blood
43	chr2:172808800-172812400	Strong transcription	HepG2	liver
44	chr2:172808800-172814000	Strong transcription	Fetal Thymus	thymus
45	chr2:172809000-172812400	Weak transcription	Psoas Muscle	Psoas
46	chr2:172809000-172822600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr2:172809200-172812600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:172809400-172813200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:172809400-172813600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:172809400-172814000	Strong transcription	Fetal Muscle Leg	muscle

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