Variant report

Variant	rs7942733
Chromosome Location	chr11:18601734-18601735
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18599363..18605712-chr11:18606522..18612149,6	MCF-7	breast:
2	chr11:18597269..18603847-chr11:18605648..18613112,11	MCF-7	breast:
3	chr11:18556808..18558328-chr11:18600770..18602452,2	MCF-7	breast:
4	chr11:18547238..18549661-chr11:18600782..18603302,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151116	Chromatin interaction
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10832939	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11024691	1.00[CEU][hapmap];0.94[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];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11024718	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11600246	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12223260	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12225251	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12226584	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935476	0.92[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];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[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];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305167	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]
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];0.94[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	0.85[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	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4756951	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[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	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4757672	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56104322	0.81[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	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72876754	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72876774	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7483340	0.87[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];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7942733	LDHC	cis	Whole Blood	GTEx
rs7942733	LDHC	cis	Muscle Skeletal	GTEx
rs7942733	LDHC	cis	Adipose Subcutaneous	GTEx
rs7942733	LDHC	cis	Artery Tibial	GTEx
rs7942733	LDHC	cis	uninvolved skin	skin_eQTL
rs7942733	LDHC	cis	lung	GTEx
rs7942733	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs7942733	LDHC	cis	Nerve Tibial	GTEx

Chromatin state (count:109 , 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	chr11:18563800-18608800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:18565200-18609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:18574400-18609400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:18575000-18609200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:18575200-18609200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:18578000-18608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:18578000-18609000	Weak transcription	Right Ventricle	heart
11	chr11:18578200-18609000	Weak transcription	Primary T cells from cord blood	blood
12	chr11:18578400-18609000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:18578600-18608400	Weak transcription	Psoas Muscle	Psoas
14	chr11:18580000-18608600	Weak transcription	Hela-S3	cervix
15	chr11:18580200-18608600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr11:18581000-18609000	Weak transcription	Pancreas	Pancrea
17	chr11:18583000-18608200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:18583000-18609400	Weak transcription	Esophagus	oesophagus
19	chr11:18583200-18604600	Weak transcription	Gastric	stomach
20	chr11:18584200-18608000	Weak transcription	Small Intestine	intestine
21	chr11:18584400-18609800	Weak transcription	Spleen	Spleen
22	chr11:18585800-18608600	Weak transcription	Fetal Brain Female	brain
23	chr11:18586400-18609000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr11:18588200-18608800	Weak transcription	Fetal Kidney	kidney
25	chr11:18591800-18608800	Weak transcription	NHEK	skin
26	chr11:18592200-18609000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr11:18592200-18609400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:18593000-18608200	Weak transcription	Brain Germinal Matrix	brain
29	chr11:18593400-18608600	Weak transcription	Dnd41	blood
30	chr11:18593600-18609400	Weak transcription	Aorta	Aorta
31	chr11:18594800-18608800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:18594800-18609000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr11:18595000-18608600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:18595000-18609000	Weak transcription	Primary B cells from cord blood	blood
35	chr11:18595200-18609200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:18595800-18608800	Weak transcription	NHLF	lung
37	chr11:18596400-18608400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:18597200-18608000	Weak transcription	Brain Hippocampus Middle	brain
39	chr11:18597200-18608800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:18597200-18609000	Weak transcription	Fetal Thymus	thymus
41	chr11:18597400-18608400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:18597400-18608600	Weak transcription	HMEC	breast
43	chr11:18597600-18608600	Weak transcription	Brain Anterior Caudate	brain
44	chr11:18597600-18608800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:18597600-18608800	Weak transcription	Brain Substantia Nigra	brain
46	chr11:18597600-18608800	Weak transcription	HUVEC	blood vessel
47	chr11:18598400-18608800	Weak transcription	Thymus	Thymus
48	chr11:18598800-18605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:18598800-18608400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr11:18599000-18608800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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