Variant report

Variant	rs10832939
Chromosome Location	chr11:18530047-18530048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18527234..18530120-chr11:18547134..18549808,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-UEVLD-2	chr11:18530031-18530367	ENSG00000256588.1

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10500836	0.80[YRI][hapmap]
rs10832940	0.86[YRI][hapmap]
rs11024691	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];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11024709	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024718	0.90[ASN][1000 genomes]
rs11600246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11603992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223260	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12224694	0.87[YRI][hapmap]
rs12225251	0.90[ASN][1000 genomes]
rs12226584	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12419063	0.80[YRI][hapmap]
rs12577346	0.83[YRI][hapmap]
rs1395319	0.82[YRI][hapmap]
rs1395320	0.84[YRI][hapmap]
rs16935476	0.92[JPT][hapmap]
rs16935482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16935488	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16935538	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16935539	0.92[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2088183	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2088184	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]
rs2292176	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305167	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3802965	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3802966	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3925781	0.80[YRI][hapmap]
rs4298881	0.80[YRI][hapmap]
rs4390325	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417245	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4636650	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4756948	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4756951	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs4757669	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757671	0.90[ASN][1000 genomes]
rs4757672	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56104322	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56138729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56991251	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6486431	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][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]
rs6486434	0.84[YRI][hapmap]
rs6486435	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7105889	0.84[YRI][hapmap]
rs7107057	0.84[YRI][hapmap]
rs72876754	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72876774	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7483340	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7928508	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7928872	0.80[YRI][hapmap]
rs7931630	0.80[YRI][hapmap]
rs7942733	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[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	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
5	nsv467719	chr11:18447611-18542227	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv553634	chr11:18447611-18542227	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs10832939	TSG101	cis	lymphoblastoid	seeQTL
rs10832939	LDHC	cis	parietal	SCAN
rs10832939	LDHC	cis	Adipose Subcutaneous	GTEx
rs10832939	LDHC	cis	Whole Blood	GTEx
rs10832939	LDHC	cis	uninvolved skin	skin_eQTL
rs10832939	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs10832939	LDHC	cis	Nerve Tibial	GTEx
rs10832939	LDHC	cis	Muscle Skeletal	GTEx
rs10832939	RPS13	cis	parietal	SCAN
rs10832939	LDHC	cis	Artery Tibial	GTEx
rs10832939	TSG101	cis	multi-tissue	Pritchard
rs10832939	LDHC	cis	lymphoblastoid	seeQTL
rs10832939	LDHC	cis	lung	GTEx
rs10832939	LDHC	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18496200-18538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:18504000-18540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:18505200-18531800	Weak transcription	Fetal Brain Male	brain
9	chr11:18509000-18537600	Strong transcription	Liver	Liver
10	chr11:18509000-18540200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:18509000-18540600	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr11:18509600-18540200	Strong transcription	Placenta	Placenta
13	chr11:18510800-18541400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr11:18513000-18544000	Weak transcription	Gastric	stomach
15	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
16	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr11:18513200-18532600	Weak transcription	Esophagus	oesophagus
18	chr11:18514600-18540800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:18514800-18539800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:18515000-18537600	Strong transcription	Fetal Thymus	thymus
21	chr11:18515000-18540000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:18515000-18540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:18515200-18538000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
25	chr11:18515600-18537600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr11:18515600-18537800	Strong transcription	Fetal Intestine Large	intestine
27	chr11:18516200-18538200	Strong transcription	Adipose Nuclei	Adipose
28	chr11:18516200-18538800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr11:18516200-18540400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr11:18516400-18531400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:18516400-18532200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:18516400-18540400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:18516800-18541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:18517200-18540400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:18517600-18534200	Strong transcription	Primary hematopoietic stem cells	blood
36	chr11:18518000-18539200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:18518200-18538600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr11:18518200-18540400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:18518400-18530400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:18518600-18531800	Weak transcription	Aorta	Aorta
41	chr11:18518600-18537200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:18519200-18531400	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr11:18519200-18540600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr11:18519200-18540800	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr11:18519200-18540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr11:18519400-18540400	Strong transcription	Primary T cells from cord blood	blood
47	chr11:18520600-18534800	Weak transcription	Right Ventricle	heart
48	chr11:18521200-18537400	Strong transcription	Primary B cells from cord blood	blood
49	chr11:18521400-18530800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:18521400-18540800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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