Variant report

Variant	rs6486435
Chromosome Location	chr11:18576878-18576879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10832939	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11024691	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024709	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024718	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600246	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11603992	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11606375	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12223260	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225251	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12226584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935482	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16935488	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16935538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088183	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2088184	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292176	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305167	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802965	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802966	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4390325	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4417245	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4636650	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4756948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756951	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4757669	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4757671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4757672	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56104322	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56138729	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56991251	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6486431	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72876754	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7483340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7942733	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
4	nsv1046886	chr11:18547568-18781448	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv540956	chr11:18547568-18781448	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv975324	chr11:18563800-18581423	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv972915	chr11:18571883-18591969	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6486435	LDHC	cis	Adipose Subcutaneous	GTEx
rs6486435	LDHC	cis	Nerve Tibial	GTEx
rs6486435	LDHC	cis	Muscle Skeletal	GTEx
rs6486435	LDHC	cis	Artery Tibial	GTEx
rs6486435	LDHC	cis	Whole Blood	GTEx
rs6486435	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs6486435	LDHC	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549000-18577000	Weak transcription	Spleen	Spleen
2	chr11:18549200-18577000	Weak transcription	Esophagus	oesophagus
3	chr11:18549200-18583400	Weak transcription	Small Intestine	intestine
4	chr11:18549200-18591400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:18549400-18577000	Weak transcription	Colonic Mucosa	Colon
6	chr11:18549400-18579200	Weak transcription	Pancreas	Pancrea
7	chr11:18549400-18583400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:18549400-18594400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:18549600-18577200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:18549600-18577800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
12	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
14	chr11:18549800-18577000	Weak transcription	Primary T cells from cord blood	blood
15	chr11:18549800-18582400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:18549800-18588200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:18549800-18592000	Weak transcription	NHLF	lung
18	chr11:18549800-18594400	Weak transcription	K562	blood
19	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr11:18550600-18591400	Weak transcription	Dnd41	blood
21	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr11:18555800-18582800	Weak transcription	NHEK	skin
23	chr11:18558400-18592200	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:18559200-18592800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
26	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr11:18564000-18586400	Weak transcription	GM12878-XiMat	blood
29	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr11:18566200-18577000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr11:18566200-18580800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr11:18566600-18577000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:18567200-18594600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
36	chr11:18567800-18588200	Strong transcription	Adipose Nuclei	Adipose
37	chr11:18568600-18577200	Weak transcription	Thymus	Thymus
38	chr11:18568600-18579200	Weak transcription	HepG2	liver
39	chr11:18568600-18591000	Weak transcription	HMEC	breast
40	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr11:18569000-18577200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr11:18569000-18577200	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr11:18569800-18577000	Weak transcription	Aorta	Aorta
44	chr11:18570000-18577400	Weak transcription	HUVEC	blood vessel
45	chr11:18571000-18577400	Weak transcription	HSMM	muscle
46	chr11:18571000-18579200	Weak transcription	NHDF-Ad	bronchial
47	chr11:18571200-18585600	Strong transcription	Fetal Stomach	stomach
48	chr11:18571400-18585200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr11:18571800-18580000	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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