Variant report

Variant	rs2088184
Chromosome Location	chr11:18543853-18543854
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18538795..18541461-chr11:18542619..18545172,2	K562	blood:
2	chr11:18528948..18532458-chr11:18541566..18545702,3	K562	blood:
3	chr11:18538359..18545865-chr11:18546460..18550640,13	MCF-7	breast:
4	chr11:18511993..18514415-chr11:18543719..18545830,2	K562	blood:
5	chr11:18539804..18546267-chr11:18546399..18550608,13	K562	blood:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction
ENSG00000256588	Chromatin interaction
ENSG00000256464	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10500836	0.80[YRI][hapmap]
rs10832939	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11024691	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11024709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024718	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11600246	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11603992	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11606375	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12223260	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12224694	0.84[YRI][hapmap]
rs12225251	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12226584	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577346	0.83[YRI][hapmap]
rs16935476	0.90[JPT][hapmap]
rs16935482	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16935488	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16935538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16935539	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2088183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292176	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2305167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3802965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802966	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3925781	0.80[YRI][hapmap]
rs4390325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417245	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4636650	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4756948	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756951	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757669	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757671	0.89[AFR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757672	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56104322	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56138729	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56991251	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6486431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6486434	0.84[YRI][hapmap]
rs6486435	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7105889	0.84[YRI][hapmap]
rs7107057	0.84[YRI][hapmap]
rs72876754	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72876774	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7483340	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7928872	0.80[YRI][hapmap]
rs7942733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv1038015	chr11:18435855-18558211	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1042155	chr11:18435855-18697576	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2088184	TSG101	cis	multi-tissue	Pritchard
rs2088184	LDHC	cis	uninvolved skin	skin_eQTL
rs2088184	LDHC	cis	Muscle Skeletal	GTEx
rs2088184	LDHC	cis	Artery Tibial	GTEx
rs2088184	LDHC	cis	Nerve Tibial	GTEx
rs2088184	LDHC	cis	lung	GTEx
rs2088184	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs2088184	LDHC	cis	Adipose Subcutaneous	GTEx
rs2088184	LDHC	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr11:18513000-18544000	Weak transcription	Gastric	stomach
3	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
4	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
6	chr11:18523800-18547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr11:18524200-18547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr11:18524200-18547400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:18527200-18547200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:18527600-18545400	Weak transcription	Small Intestine	intestine
11	chr11:18531200-18544600	Weak transcription	Hela-S3	cervix
12	chr11:18531400-18546600	Weak transcription	K562	blood
13	chr11:18532800-18547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:18533400-18547200	Weak transcription	A549	lung
15	chr11:18534800-18547200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:18535400-18547800	Weak transcription	Esophagus	oesophagus
17	chr11:18535600-18544000	Weak transcription	Spleen	Spleen
18	chr11:18535600-18544200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr11:18535600-18546600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:18535600-18547600	Weak transcription	Aorta	Aorta
21	chr11:18535800-18544000	Weak transcription	Left Ventricle	heart
22	chr11:18535800-18544000	Weak transcription	Ovary	ovary
23	chr11:18535800-18545800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr11:18535800-18546200	Weak transcription	Right Ventricle	heart
25	chr11:18535800-18547200	Weak transcription	HUVEC	blood vessel
26	chr11:18535800-18547400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr11:18535800-18547800	Weak transcription	Lung	lung
28	chr11:18536000-18544200	Weak transcription	Fetal Muscle Leg	muscle
29	chr11:18536000-18546200	Weak transcription	Thymus	Thymus
30	chr11:18536200-18547200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr11:18536200-18547200	Weak transcription	HSMMtube	muscle
32	chr11:18536400-18544000	Weak transcription	HepG2	liver
33	chr11:18536400-18544200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr11:18536400-18545800	Weak transcription	GM12878-XiMat	blood
35	chr11:18536600-18547200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:18536800-18547400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:18537200-18545600	Weak transcription	NH-A	brain
38	chr11:18537200-18546800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:18537200-18547400	Weak transcription	Colonic Mucosa	Colon
40	chr11:18537400-18544600	Weak transcription	NHEK	skin
41	chr11:18537400-18545600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr11:18537400-18546200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr11:18537400-18547200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:18537400-18547200	Weak transcription	Brain Angular Gyrus	brain
45	chr11:18537400-18547200	Weak transcription	Brain Substantia Nigra	brain
46	chr11:18537400-18547200	Weak transcription	NHLF	lung
47	chr11:18537400-18547400	Weak transcription	Brain Anterior Caudate	brain
48	chr11:18537400-18547600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr11:18537600-18544200	Weak transcription	HMEC	breast
50	chr11:18537600-18546800	Weak transcription	Fetal Brain Male	brain

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