Variant report

Variant	rs2305167
Chromosome Location	chr11:18596580-18596581
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18596231..18598962-chr11:18654372..18657232,2	MCF-7	breast:
2	chr11:18594808..18597931-chr11:18609017..18611085,3	MCF-7	breast:
3	chr11:18595002..18597166-chr11:18603669..18605204,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151116	Chromatin interaction
ENSG00000179119	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10832939	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11024691	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11024709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024718	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600246	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11603992	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11606375	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12223260	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225251	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12226584	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935476	0.91[JPT][hapmap]
rs16935482	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16935488	0.88[ASN][1000 genomes]
rs16935538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935539	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2088183	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2088184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2292176	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3802965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3802966	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4390325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4417245	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4636650	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4756948	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756951	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4757669	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4757671	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4757672	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56104322	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56138729	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56991251	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6486431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6486435	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72876754	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876774	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7483340	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7928508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7942733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3442757	chr11:18595343-18596606	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2305167	LDHC	cis	Nerve Tibial	GTEx
rs2305167	LDHC	cis	Muscle Skeletal	GTEx
rs2305167	LDHC	cis	Adipose Subcutaneous	GTEx
rs2305167	LDHC	cis	Artery Tibial	GTEx
rs2305167	LDHC	cis	Whole Blood	GTEx
rs2305167	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs2305167	LDHC	cis	lung	GTEx
rs2305167	LDHC	cis	uninvolved skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18549600-18608600	Weak transcription	Fetal Heart	heart
2	chr11:18549600-18609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:18549600-18609000	Weak transcription	Fetal Brain Male	brain
4	chr11:18549800-18600600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:18552600-18601400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:18562200-18598200	Weak transcription	Stomach Mucosa	stomach
7	chr11:18563200-18601200	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:18566200-18601000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr11:18567400-18601000	Strong transcription	Placenta	Placenta
12	chr11:18568600-18600800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:18571800-18601200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr11:18576800-18599200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:18577400-18599200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr11:18578000-18600600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
22	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
23	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
25	chr11:18579600-18600800	Weak transcription	Colonic Mucosa	Colon
26	chr11:18580000-18608600	Weak transcription	Hela-S3	cervix
27	chr11:18580200-18608600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:18581000-18609000	Weak transcription	Pancreas	Pancrea
29	chr11:18582600-18600600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr11:18583000-18608200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr11:18583000-18609400	Weak transcription	Esophagus	oesophagus
32	chr11:18583200-18597000	Weak transcription	Brain Substantia Nigra	brain
33	chr11:18583200-18604600	Weak transcription	Gastric	stomach
34	chr11:18584200-18600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:18584200-18608000	Weak transcription	Small Intestine	intestine
36	chr11:18584400-18609800	Weak transcription	Spleen	Spleen
37	chr11:18585000-18597400	Weak transcription	Thymus	Thymus
38	chr11:18585800-18608600	Weak transcription	Fetal Brain Female	brain
39	chr11:18586400-18609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr11:18587200-18598800	Weak transcription	GM12878-XiMat	blood
41	chr11:18587800-18598200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:18588200-18608800	Weak transcription	Fetal Kidney	kidney
43	chr11:18590000-18600000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:18590200-18601200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:18590800-18601200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:18590800-18601400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:18591000-18601200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr11:18591000-18601200	Strong transcription	Adipose Nuclei	Adipose
49	chr11:18591200-18601200	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:18591200-18601400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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