Variant report

Variant	rs7560795
Chromosome Location	chr2:100102790-100102791
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100092416..100102947-chr2:100103557..100108181,19	MCF-7	breast:
2	chr2:99952415..99954577-chr2:100101593..100103318,2	MCF-7	breast:
3	chr2:100011720..100013891-chr2:100102274..100104165,2	K562	blood:
4	chr2:100077312..100079121-chr2:100100989..100102811,2	K562	blood:
5	chr2:100077312..100079751-chr2:100099970..100102811,3	K562	blood:
6	chr2:99952384..99954745-chr2:100101155..100103970,2	K562	blood:
7	chr2:99796371..99799059-chr2:100100777..100103682,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185414	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000158417	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1000409	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1011633	0.82[ASN][1000 genomes]
rs10170425	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10172068	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10172752	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10173466	0.82[ASN][1000 genomes]
rs10186340	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11887109	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11887574	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12478488	0.81[EUR][1000 genomes]
rs13384883	0.81[AMR][1000 genomes]
rs13392042	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13394688	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13427780	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1451243	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1839666	0.81[ASN][1000 genomes]
rs1901283	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1973011	0.81[ASN][1000 genomes]
rs2242037	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2309585	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2309604	0.82[ASN][1000 genomes]
rs28369943	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28382954	0.83[AMR][1000 genomes]
rs3087386	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792134	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792146	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3792149	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3792152	0.81[EUR][1000 genomes]
rs4143760	0.82[ASN][1000 genomes]
rs4535093	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4851205	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6542879	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6542880	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6542882	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6713792	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6714244	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717515	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6737560	0.82[ASN][1000 genomes]
rs7564587	0.81[ASN][1000 genomes]
rs7567674	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7580448	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7598629	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7601730	0.81[AMR][1000 genomes]
rs896249	0.82[ASN][1000 genomes]
rs959929	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv1811477	chr2:100089078-100105013	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	esv1810220	chr2:100094799-100105013	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv1806302	chr2:100094799-100123030	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3457028	chr2:100101720-100107018	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
8	esv3487602	chr2:100102570-100106918	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
9	esv2555492	chr2:100102701-100105388	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7560795	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs7560795	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs7560795	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
2	chr2:100076200-100105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:100076600-100104200	Weak transcription	NHLF	lung
4	chr2:100078800-100103000	Weak transcription	Primary B cells from cord blood	blood
5	chr2:100078800-100105000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:100079200-100104000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:100080400-100103200	Weak transcription	Fetal Stomach	stomach
8	chr2:100080800-100103200	Weak transcription	HSMM	muscle
9	chr2:100085600-100103000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr2:100088000-100104800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:100091400-100103200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:100091800-100103400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:100092600-100103600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:100092600-100104200	Weak transcription	Osteobl	bone
15	chr2:100092800-100103600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr2:100092800-100104600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:100092800-100105000	Weak transcription	Placenta	Placenta
18	chr2:100094000-100103400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:100094800-100104800	Weak transcription	Colonic Mucosa	Colon
20	chr2:100095200-100103400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:100095400-100103400	Weak transcription	HUVEC	blood vessel
22	chr2:100095600-100103000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:100095600-100103400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr2:100095600-100103600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:100095600-100103600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:100097200-100103000	Weak transcription	NH-A	brain
27	chr2:100097200-100104000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:100097200-100104200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:100097200-100105000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:100097800-100103200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:100098000-100103200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr2:100098600-100105200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:100098600-100105200	Weak transcription	Gastric	stomach
34	chr2:100098800-100103000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:100098800-100103000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:100098800-100103000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:100098800-100103200	Weak transcription	Adipose Nuclei	Adipose
38	chr2:100098800-100103400	Weak transcription	Brain Substantia Nigra	brain
39	chr2:100098800-100103400	Weak transcription	Stomach Mucosa	stomach
40	chr2:100098800-100104800	Weak transcription	Spleen	Spleen
41	chr2:100098800-100105000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:100098800-100105200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:100099000-100103000	Weak transcription	Fetal Intestine Large	intestine
44	chr2:100099000-100103000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:100099000-100103200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:100099000-100103200	Weak transcription	Fetal Intestine Small	intestine
47	chr2:100099000-100103200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr2:100099000-100103200	Weak transcription	NHDF-Ad	bronchial
49	chr2:100099000-100103600	Weak transcription	Primary T cells from cord blood	blood
50	chr2:100099000-100103800	Weak transcription	H1 Cell Line	embryonic stem cell

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