Variant report

Variant	rs4495397
Chromosome Location	chr8:103407193-103407194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:103407170..103409937-chr8:103664243..103667320,3	MCF-7	breast:
2	chr8:103404137..103406751-chr8:103406797..103410088,3	K562	blood:
3	chr8:103404586..103407387-chr8:103414307..103417214,2	MCF-7	breast:
4	chr8:103405057..103410665-chr8:103422251..103425173,5	MCF-7	breast:
5	chr8:103406201..103411480-chr8:103421779..103426135,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155090	Chromatin interaction
ENSG00000104517	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12114277	0.82[CHB][hapmap];0.83[CHD][hapmap]
rs13248227	0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13269273	0.83[JPT][hapmap]
rs13270182	0.95[JPT][hapmap]
rs13281324	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2445950	0.82[EUR][1000 genomes]
rs2512408	0.82[CHB][hapmap]
rs2512409	0.84[CHD][hapmap]
rs2607663	0.89[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap]
rs2853232	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2853236	0.84[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs2853238	0.80[CHD][hapmap]
rs4609174	0.87[JPT][hapmap]
rs4617126	0.87[CHB][hapmap]
rs4734619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62523127	0.81[ASN][1000 genomes]
rs6468826	0.87[CHB][hapmap]
rs71209870	0.82[ASN][1000 genomes]
rs7823262	0.80[ASN][1000 genomes]
rs7827839	0.87[CHB][hapmap];0.83[CHD][hapmap]
rs7829887	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9642790	0.80[ASN][1000 genomes]
rs9693239	0.87[JPT][hapmap]
rs9694458	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv891244	chr8:103309862-103483466	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv831412	chr8:103337196-103536397	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
6	nsv1023938	chr8:103369215-103538708	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	esv2761454	chr8:103394602-103414235	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4495397	ATP6V1C1	cis	parietal	SCAN
rs4495397	UBR5	Cis_1M	lymphoblastoid	RTeQTL
rs4495397	PABPC1	cis	cerebellum	SCAN
rs4495397	LOC730429///UBR5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103369800-103421000	Weak transcription	Colonic Mucosa	Colon
2	chr8:103372400-103412600	Weak transcription	Fetal Intestine Large	intestine
3	chr8:103372800-103410200	Weak transcription	Fetal Kidney	kidney
4	chr8:103384200-103411600	Weak transcription	Lung	lung
5	chr8:103384200-103416800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:103388200-103407200	Weak transcription	Right Ventricle	heart
7	chr8:103388400-103416600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:103394600-103407200	Weak transcription	Pancreas	Pancrea
9	chr8:103395600-103407200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr8:103395800-103420800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:103395800-103422200	Weak transcription	HSMMtube	muscle
12	chr8:103396000-103410200	Weak transcription	Brain Germinal Matrix	brain
13	chr8:103396200-103407200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr8:103396200-103407400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:103396200-103408200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr8:103396200-103409600	Weak transcription	Fetal Stomach	stomach
17	chr8:103396800-103407400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr8:103397000-103413600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:103397200-103408000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr8:103397400-103420800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr8:103397800-103408400	Weak transcription	Fetal Brain Female	brain
22	chr8:103398600-103420800	Weak transcription	Esophagus	oesophagus
23	chr8:103399800-103408200	Weak transcription	Psoas Muscle	Psoas
24	chr8:103400000-103408000	Weak transcription	Fetal Intestine Small	intestine
25	chr8:103400400-103407800	Weak transcription	A549	lung
26	chr8:103400800-103414800	Weak transcription	HUVEC	blood vessel
27	chr8:103403400-103407200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr8:103403400-103407400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr8:103403400-103407400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr8:103403400-103407400	Weak transcription	Thymus	Thymus
31	chr8:103403400-103407800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr8:103403400-103408000	Weak transcription	Fetal Lung	lung
33	chr8:103403400-103408600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr8:103403400-103408800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr8:103403400-103409800	Weak transcription	Fetal Thymus	thymus
36	chr8:103403400-103410400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr8:103403400-103410400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr8:103403400-103410400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr8:103403400-103410400	Weak transcription	Fetal Muscle Leg	muscle
40	chr8:103403400-103412400	Weak transcription	Dnd41	blood
41	chr8:103403400-103412400	Weak transcription	NHEK	skin
42	chr8:103403400-103413600	Weak transcription	Gastric	stomach
43	chr8:103403400-103416800	Weak transcription	Placenta	Placenta
44	chr8:103403400-103420000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr8:103403400-103423000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:103403600-103410600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:103404000-103412200	Weak transcription	Hela-S3	cervix
48	chr8:103404200-103407200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr8:103404200-103407200	Weak transcription	Ovary	ovary
50	chr8:103404200-103410000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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