Variant report

Variant	rs1395319
Chromosome Location	chr11:18548183-18548184
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:18548142..18548670-chr11:18609940..18610633,2	MCF-7	breast:
2	chr11:18546372..18549758-chr11:18653531..18658575,7	K562	blood:
3	chr1:225117317..225117947-chr11:18547900..18548603,2	NB4	blood:
4	chr1:159894571..159895309-chr11:18547917..18548843,2	Hela-S3	cervix:
5	chr11:18546581..18551368-chr11:18654825..18657467,6	K562	blood:
6	chr11:18502477..18505271-chr11:18547847..18549412,2	K562	blood:
7	chr11:18342189..18343915-chr11:18546820..18548379,2	MCF-7	breast:
8	chr11:18341846..18344494-chr11:18547115..18549354,2	MCF-7	breast:
9	chr11:18548007..18548707-chr15:89877506..89878449,2	Hela-S3	cervix:
10	chr11:18547695..18548426-chr5:149379662..149380630,2	Hela-S3	cervix:
11	chr11:18432193..18433875-chr11:18547475..18550164,2	MCF-7	breast:
12	chr11:18547238..18549661-chr11:18600782..18603302,3	MCF-7	breast:
13	chr11:18548103..18548963-chr18:12702273..12702811,2	Hela-S3	cervix:
14	chr11:18414795..18417618-chr11:18546727..18549809,4	MCF-7	breast:
15	chr11:18546303..18549278-chr11:18609985..18612598,2	K562	blood:
16	chr11:18547695..18548456-chr22:46449860..46450463,2	Hela-S3	cervix:
17	chr11:18343253..18347316-chr11:18546908..18550670,5	K562	blood:
18	chr11:18533507..18535848-chr11:18546408..18548301,3	K562	blood:
19	chr1:1334202..1334912-chr11:18547765..18548751,2	Hela-S3	cervix:
20	chr1:36396047..36396934-chr11:18547924..18549049,4	Hela-S3	cervix:
21	chr11:18531181..18534158-chr11:18547173..18549352,2	MCF-7	breast:
22	chr11:18547936..18548865-chr12:1800180..1800752,2	Hela-S3	cervix:
23	chr10:70091815..70092544-chr11:18548061..18548917,2	Hela-S3	cervix:
24	chr11:18415765..18417941-chr11:18547561..18549649,2	K562	blood:
25	chr11:18546489..18551340-chr11:18552893..18563258,14	MCF-7	breast:
26	chr11:18548173..18549021-chr5:1633797..1634587,2	Hela-S3	cervix:
27	chr11:18548066..18548848-chr20:48789021..48789605,2	Hela-S3	cervix:
28	chr11:18547881..18548707-chr21:44313013..44313598,2	Hela-S3	cervix:
29	chr11:18415399..18418482-chr11:18547632..18550708,3	MCF-7	breast:
30	chr11:18548038..18548586-chr5:34915319..34916073,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000110756	Chromatin interaction
ENSG00000113716	Chromatin interaction
ENSG00000241990	Chromatin interaction
ENSG00000140521	Chromatin interaction
ENSG00000158710	Chromatin interaction
ENSG00000151116	Chromatin interaction
ENSG00000110768	Chromatin interaction
ENSG00000113460	Chromatin interaction
ENSG00000074319	Chromatin interaction
ENSG00000261441	Chromatin interaction
ENSG00000185842	Chromatin interaction
ENSG00000188002	Chromatin interaction
ENSG00000224870	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000126070	Chromatin interaction
ENSG00000179119	Chromatin interaction
ENSG00000221978	Chromatin interaction
ENSG00000164296	Chromatin interaction
ENSG00000006831	Chromatin interaction
ENSG00000160194	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000166796	Chromatin interaction
ENSG00000113456	Chromatin interaction
ENSG00000182257	Chromatin interaction
ENSG00000231742	Chromatin interaction
ENSG00000096746	Chromatin interaction
ENSG00000256361	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10500836	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10741747	0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10766483	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10766484	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10766485	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832939	0.82[YRI][hapmap]
rs10832940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10832941	0.85[JPT][hapmap]
rs11024690	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11024699	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024717	0.85[JPT][hapmap]
rs12224694	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12225037	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12419063	0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12574808	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12577346	0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1395320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16935538	0.82[YRI][hapmap]
rs1857907	0.92[JPT][hapmap]
rs2132302	0.92[JPT][hapmap]
rs2658552	0.85[JPT][hapmap]
rs2658564	0.84[JPT][hapmap]
rs34457574	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3925781	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4298881	0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4623881	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756949	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756950	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4756952	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56333121	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6486430	0.85[JPT][hapmap]
rs6486431	0.82[YRI][hapmap]
rs6486434	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7105889	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7107057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7119085	1.00[JPT][hapmap]
rs7129164	0.92[JPT][hapmap]
rs7928872	1.00[JPT][hapmap];0.95[YRI][hapmap]
rs7931630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934817	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7951508	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7952284	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868069	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	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
6	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1395319	TSG101	cis	multi-tissue	Pritchard
rs1395319	LDHC	cis	Thyroid	GTEx
rs1395319	TSG101	Cis_1M	lymphoblastoid	RTeQTL
rs1395319	TSG101	cis	Esophagus Mucosa	GTEx
rs1395319	TSG101	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18547000-18549000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr11:18547000-18549200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:18547000-18549600	Active TSS	GM12878-XiMat	blood
4	chr11:18547200-18548600	Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr11:18547200-18548600	Active TSS	HMEC	breast
6	chr11:18547200-18549000	Active TSS	Muscle Satellite Cultured Cells	--
7	chr11:18547200-18549000	Active TSS	Brain Substantia Nigra	brain
8	chr11:18547200-18549000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr11:18547200-18549000	Active TSS	Fetal Stomach	stomach
10	chr11:18547200-18549200	Active TSS	Fetal Brain Female	brain
11	chr11:18547200-18549400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr11:18547200-18549600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr11:18547200-18549600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr11:18547200-18549600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr11:18547200-18549600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr11:18547200-18549600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr11:18547200-18549600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr11:18547200-18549600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:18547200-18549600	Active TSS	Fetal Intestine Large	intestine
20	chr11:18547200-18549600	Active TSS	K562	blood
21	chr11:18547200-18549800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:18547200-18549800	Active TSS	Psoas Muscle	Psoas
23	chr11:18547200-18549800	Active TSS	Stomach Smooth Muscle	stomach
24	chr11:18547400-18548800	Active TSS	Hela-S3	cervix
25	chr11:18547400-18548800	Active TSS	HepG2	liver
26	chr11:18547400-18549000	Active TSS	Fetal Muscle Leg	muscle
27	chr11:18547400-18549000	Active TSS	Fetal Thymus	thymus
28	chr11:18547400-18549200	Active TSS	Placenta	Placenta
29	chr11:18547400-18549400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr11:18547400-18549400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr11:18547400-18549400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr11:18547400-18549400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:18547400-18549400	Active TSS	Colonic Mucosa	Colon
34	chr11:18547400-18549400	Active TSS	Fetal Intestine Small	intestine
35	chr11:18547400-18549400	Active TSS	Fetal Muscle Trunk	muscle
36	chr11:18547400-18549400	Active TSS	Ovary	ovary
37	chr11:18547400-18549400	Active TSS	Right Atrium	heart
38	chr11:18547400-18549600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:18547400-18549600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr11:18547400-18549600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr11:18547400-18549600	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr11:18547400-18549600	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr11:18547400-18549600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr11:18547400-18549600	Active TSS	HSMMtube	muscle
45	chr11:18547400-18549800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:18547400-18549800	Active TSS	Right Ventricle	heart
47	chr11:18547400-18549800	Active TSS	A549	lung
48	chr11:18547600-18548200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr11:18547600-18548400	Active TSS	Dnd41	blood
50	chr11:18547600-18548600	Active TSS	HUVEC	blood vessel

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