Variant report

Variant	rs7434107
Chromosome Location	chr3:48541182-48541183
allele	A/G
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48519627..48521356-chr3:48540019..48542840,2	MCF-7	breast:
2	chr3:48512987..48515121-chr3:48538907..48542764,4	MCF-7	breast:
3	chr3:48486835..48489928-chr3:48540255..48543800,6	MCF-7	breast:
4	chr3:48541156..48543765-chr3:48670075..48672910,2	K562	blood:
5	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:
6	chr3:48506549..48509845-chr3:48539899..48542681,4	MCF-7	breast:
7	chr3:48540167..48542954-chr3:48592530..48594484,3	MCF-7	breast:
8	chr3:48511787..48515469-chr3:48539737..48543035,4	K562	blood:
9	chr3:48481573..48483213-chr3:48538855..48541265,2	MCF-7	breast:
10	chr3:48540047..48541842-chr3:48700022..48702495,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213689	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000164053	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10049154	0.95[ASN][1000 genomes]
rs10470687	0.82[ASN][1000 genomes]
rs12492271	0.82[AFR][1000 genomes]
rs13060933	0.81[ASN][1000 genomes]
rs13062576	0.97[ASN][1000 genomes]
rs13064619	0.95[ASN][1000 genomes]
rs13091944	0.85[ASN][1000 genomes]
rs13094578	1.00[ASN][1000 genomes]
rs13100178	1.00[ASN][1000 genomes]
rs13319635	0.81[ASN][1000 genomes]
rs13319651	0.81[ASN][1000 genomes]
rs2006871	0.85[ASN][1000 genomes]
rs28563843	0.86[ASN][1000 genomes]
rs28881595	0.94[ASN][1000 genomes]
rs35562294	0.82[ASN][1000 genomes]
rs3755819	0.82[ASN][1000 genomes]
rs3969942	1.00[ASN][1000 genomes]
rs4075082	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6442127	0.98[ASN][1000 genomes]
rs6765317	0.94[ASN][1000 genomes]
rs6781283	0.81[ASN][1000 genomes]
rs6785845	0.95[ASN][1000 genomes]
rs6786424	0.82[ASN][1000 genomes]
rs6792525	0.82[ASN][1000 genomes]
rs6806059	0.88[ASN][1000 genomes]
rs6809981	0.95[ASN][1000 genomes]
rs7428949	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434077	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7623614	1.00[ASN][1000 genomes]
rs7640031	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644771	1.00[ASN][1000 genomes]
rs9810549	0.86[ASN][1000 genomes]
rs9810991	0.86[ASN][1000 genomes]
rs9816942	1.00[ASN][1000 genomes]
rs9822677	0.95[ASN][1000 genomes]
rs9835827	0.95[ASN][1000 genomes]
rs9835902	0.98[ASN][1000 genomes]
rs9837687	0.86[ASN][1000 genomes]
rs9848824	0.86[ASN][1000 genomes]
rs9849280	0.86[ASN][1000 genomes]
rs9850102	0.88[ASN][1000 genomes]
rs9851743	1.00[ASN][1000 genomes]
rs9851771	1.00[ASN][1000 genomes]
rs9864729	0.86[ASN][1000 genomes]
rs9869698	0.86[ASN][1000 genomes]
rs9871180	0.80[ASN][1000 genomes]
rs9871608	1.00[ASN][1000 genomes]
rs9878950	0.81[ASN][1000 genomes]
rs9881877	0.82[ASN][1000 genomes]
rs9882962	0.81[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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7434107	SHISA5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48533200-48541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:48539800-48541400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr3:48540000-48541400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:48540000-48541400	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr3:48540000-48541400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr3:48540000-48541400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr3:48540200-48541200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:48540200-48541200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:48540200-48541200	Flanking Active TSS	Brain Angular Gyrus	brain
10	chr3:48540200-48541200	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr3:48540200-48541200	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr3:48540200-48541200	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr3:48540200-48541200	Flanking Active TSS	Osteobl	bone
14	chr3:48540200-48541400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:48540200-48541400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:48540200-48541400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr3:48540200-48541400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:48540200-48541400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr3:48540200-48542400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:48540400-48541200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr3:48540400-48541200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr3:48540400-48541200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:48540400-48541200	Flanking Bivalent TSS/Enh	HepG2	liver
24	chr3:48540400-48541200	Flanking Active TSS	K562	blood
25	chr3:48540400-48541400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr3:48540400-48541400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:48540400-48541400	Flanking Active TSS	Liver	Liver
28	chr3:48540400-48541400	Flanking Active TSS	Colonic Mucosa	Colon
29	chr3:48540400-48541400	Flanking Active TSS	Fetal Muscle Leg	muscle
30	chr3:48540400-48541400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
31	chr3:48540400-48541400	Flanking Active TSS	Right Ventricle	heart
32	chr3:48540400-48541400	Flanking Active TSS	NH-A	brain
33	chr3:48540400-48542000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:48540600-48541200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr3:48540600-48541200	Flanking Active TSS	Fetal Intestine Small	intestine
36	chr3:48540600-48541200	Enhancers	Fetal Lung	lung
37	chr3:48540600-48541200	Flanking Active TSS	Stomach Mucosa	stomach
38	chr3:48540600-48541200	Flanking Active TSS	NHEK	skin
39	chr3:48540600-48541400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
40	chr3:48540600-48541400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr3:48540600-48541400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:48540600-48541400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr3:48540600-48541400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:48540600-48541400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:48540600-48541400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
46	chr3:48540600-48541400	Flanking Active TSS	HUVEC	blood vessel
47	chr3:48540600-48541800	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr3:48540600-48542000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:48540600-48542400	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr3:48540800-48541200	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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