Variant report

Variant	rs34457574
Chromosome Location	chr11:18540574-18540575
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:18535996..18538848-chr11:18539751..18543150,4	MCF-7	breast:
2	chr11:18538795..18541461-chr11:18542619..18545172,2	K562	blood:
3	chr11:18538359..18545865-chr11:18546460..18550640,13	MCF-7	breast:
4	chr11:18536192..18538162-chr11:18539914..18542011,2	K562	blood:
5	chr11:18540175..18542795-chr11:18547833..18549467,2	MCF-7	breast:
6	chr11:18539804..18546267-chr11:18546399..18550608,13	K562	blood:

Variant related genes	Relation type
ENSG00000074319	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10500836	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10741747	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10766483	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10766484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10766485	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832940	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024690	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024699	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11024711	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12224694	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12225037	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419063	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574808	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12577346	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395319	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1395320	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3925781	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4298881	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4623881	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756949	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756950	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756952	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56333121	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6486434	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7105889	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107057	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7928872	0.80[AMR][1000 genomes]
rs7931630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7934817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7951508	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7952284	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868069	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34457574	TSG101	cis	multi-tissue	Pritchard
rs34457574	LDHC	cis	Thyroid	GTEx
rs34457574	TSG101	cis	Esophagus Mucosa	GTEx
rs34457574	TSG101	cis	Muscle Skeletal	GTEx
rs34457574	TSG101	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18496200-18541200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr11:18496400-18542000	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr11:18496600-18540600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:18496600-18541000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr11:18500000-18547000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:18504000-18540600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:18509000-18540600	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:18510800-18541400	Strong transcription	Primary B cells from peripheral blood	blood
9	chr11:18513000-18544000	Weak transcription	Gastric	stomach
10	chr11:18513000-18544000	Weak transcription	Psoas Muscle	Psoas
11	chr11:18513000-18547600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:18514600-18540800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:18515000-18540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:18515400-18547200	Weak transcription	Stomach Mucosa	stomach
15	chr11:18516800-18541800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:18519200-18540600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr11:18519200-18540800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr11:18519200-18540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:18521400-18540800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:18523800-18547400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr11:18524200-18547200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:18524200-18547400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:18526000-18540800	Strong transcription	Fetal Brain Female	brain
24	chr11:18527200-18547200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:18527600-18545400	Weak transcription	Small Intestine	intestine
26	chr11:18531200-18540600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr11:18531200-18544600	Weak transcription	Hela-S3	cervix
28	chr11:18531400-18546600	Weak transcription	K562	blood
29	chr11:18532800-18547400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:18533400-18547200	Weak transcription	A549	lung
31	chr11:18534800-18547200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:18535000-18543400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr11:18535400-18547800	Weak transcription	Esophagus	oesophagus
34	chr11:18535600-18544000	Weak transcription	Spleen	Spleen
35	chr11:18535600-18544200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr11:18535600-18546600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr11:18535600-18547600	Weak transcription	Aorta	Aorta
38	chr11:18535800-18544000	Weak transcription	Left Ventricle	heart
39	chr11:18535800-18544000	Weak transcription	Ovary	ovary
40	chr11:18535800-18545800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr11:18535800-18546200	Weak transcription	Right Ventricle	heart
42	chr11:18535800-18547200	Weak transcription	HUVEC	blood vessel
43	chr11:18535800-18547400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr11:18535800-18547800	Weak transcription	Lung	lung
45	chr11:18536000-18543200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:18536000-18544200	Weak transcription	Fetal Muscle Leg	muscle
47	chr11:18536000-18546200	Weak transcription	Thymus	Thymus
48	chr11:18536200-18547200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr11:18536200-18547200	Weak transcription	HSMMtube	muscle
50	chr11:18536400-18544000	Weak transcription	HepG2	liver

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