Variant report

Variant	rs1077181
Chromosome Location	chr3:141174956-141174957
allele	A/C
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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:141083112..141085653-chr3:141174087..141176079,2	MCF-7	breast:
2	chr3:141086425..141088887-chr3:141174071..141176856,2	K562	blood:
3	chr3:141025929..141033510-chr3:141171081..141179408,10	MCF-7	breast:
4	chr3:141119971..141122596-chr3:141173473..141175987,4	MCF-7	breast:
5	chr3:141085844..141090637-chr3:141172239..141176083,8	MCF-7	breast:
6	chr3:141084648..141088549-chr3:141172324..141176689,9	MCF-7	breast:
7	chr3:141138083..141140957-chr3:141173553..141175424,3	MCF-7	breast:
8	chr3:141174636..141177502-chr3:141205473..141207739,2	K562	blood:
9	chr3:141172536..141178199-chr3:141203718..141209390,5	K562	blood:
10	chr3:141126713..141129325-chr3:141173577..141175312,2	MCF-7	breast:
11	chr3:141173863..141176628-chr3:141274663..141277094,3	MCF-7	breast:
12	chr3:140992139..140994461-chr3:141173161..141175634,3	MCF-7	breast:
13	chr3:141173421..141179159-chr3:141204636..141208201,13	MCF-7	breast:
14	chr3:141173783..141176363-chr3:141184238..141186556,4	MCF-7	breast:
15	chr3:141158936..141162571-chr3:141173016..141176156,4	MCF-7	breast:
16	chr3:141029860..141032097-chr3:141173989..141175746,3	K562	blood:
17	chr3:141027235..141027936-chr3:141174424..141175009,2	MCF-7	breast:
18	chr3:141173922..141177182-chr3:141288723..141292910,3	MCF-7	breast:
19	chr3:141079477..141080357-chr3:141173225..141175092,7	MCF-7	breast:
20	chr3:141172749..141175132-chr3:141195060..141197634,2	K562	blood:
21	chr3:141078564..141081479-chr3:141173622..141176571,3	MCF-7	breast:
22	chr3:141145737..141147398-chr3:141173566..141175640,2	MCF-7	breast:
23	chr3:141025955..141033087-chr3:141172047..141179174,18	MCF-7	breast:
24	chr3:141133198..141135160-chr3:141173942..141176696,2	MCF-7	breast:
25	chr3:141128423..141130797-chr3:141173455..141176523,3	MCF-7	breast:
26	chr3:141172650..141176530-chr3:141204410..141207330,5	MCF-7	breast:
27	chr3:141173524..141175043-chr3:141217283..141220078,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155893	Chromatin interaction
ENSG00000249540	Chromatin interaction
ENSG00000155903	Chromatin interaction
ENSG00000249417	Chromatin interaction
ENSG00000177311	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11707656	0.83[AMR][1000 genomes]
rs11708253	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11709875	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11714208	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs11716776	0.95[AMR][1000 genomes]
rs11717144	0.88[CEU][hapmap]
rs11717842	0.92[CEU][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes]
rs12695734	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12695735	0.91[CEU][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12695736	0.95[AMR][1000 genomes]
rs12695740	0.83[CEU][hapmap];0.92[MEX][hapmap]
rs12695741	0.84[CEU][hapmap]
rs12695743	0.85[ASW][hapmap];0.80[CEU][hapmap]
rs13059128	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13072100	0.92[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13078872	0.92[CEU][hapmap];0.89[AMR][1000 genomes]
rs13083593	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes]
rs13084444	0.92[CEU][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs13088429	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13095168	0.88[CEU][hapmap]
rs13098300	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13099945	0.88[CEU][hapmap]
rs1863870	0.96[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2312194	0.81[AMR][1000 genomes]
rs3806647	0.82[AMR][1000 genomes]
rs720663	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs7636914	0.86[ASW][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9289629	0.92[CEU][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9289634	0.88[CEU][hapmap]
rs9808953	0.88[CEU][hapmap]
rs9822575	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs9823528	0.81[AMR][1000 genomes]
rs9830055	0.88[CEU][hapmap]
rs9833121	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs9836050	0.88[CEU][hapmap]
rs9837202	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9838230	0.82[AMR][1000 genomes]
rs9838419	0.81[AMR][1000 genomes]
rs9840697	0.81[AMR][1000 genomes]
rs9849180	0.92[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes]
rs9850416	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs9865971	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs9868956	0.88[CEU][hapmap];0.81[AMR][1000 genomes]
rs9870749	0.88[CEU][hapmap];0.93[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1077181	ATP1B3	cis	cerebellum	SCAN
rs1077181	RASA2	cis	parietal	SCAN
rs1077181	TRPC1	cis	parietal	SCAN
rs1077181	ZBTB38	cis	cerebellum	SCAN
rs1077181	GK5	cis	parietal	SCAN
rs1077181	RASA2	cis	cerebellum	SCAN
rs1077181	PLSCR1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141164200-141176400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:141166600-141176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:141166600-141181600	Weak transcription	Pancreas	Pancrea
4	chr3:141166800-141176400	Weak transcription	HMEC	breast
5	chr3:141166800-141179200	Weak transcription	Fetal Brain Male	brain
6	chr3:141167400-141176600	Weak transcription	HSMM	muscle
7	chr3:141168400-141179200	Weak transcription	Fetal Heart	heart
8	chr3:141168600-141181800	Weak transcription	Aorta	Aorta
9	chr3:141169000-141179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:141171400-141179200	Weak transcription	Small Intestine	intestine
11	chr3:141171600-141179000	Weak transcription	Brain Anterior Caudate	brain
12	chr3:141172600-141175000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:141173000-141175000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:141173000-141175200	Enhancers	Fetal Stomach	stomach
15	chr3:141173000-141175400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:141173000-141175600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:141173200-141175000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:141173600-141175000	Enhancers	Fetal Intestine Small	intestine
19	chr3:141173600-141175200	Enhancers	Placenta	Placenta
20	chr3:141173800-141175000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:141173800-141175000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:141173800-141177000	Enhancers	Fetal Intestine Large	intestine
23	chr3:141174000-141175200	Flanking Active TSS	NHDF-Ad	bronchial
24	chr3:141174000-141175600	Enhancers	Fetal Lung	lung
25	chr3:141174000-141175800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:141174200-141175000	Weak transcription	Adipose Nuclei	Adipose
27	chr3:141174200-141175400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:141174200-141175600	Enhancers	Ovary	ovary
29	chr3:141174200-141176000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:141174200-141176400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:141174200-141176600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:141174200-141176600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:141174200-141179000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:141174200-141179000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:141174200-141179200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:141174200-141181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:141174200-141182200	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:141174200-141182400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:141174200-141182400	Weak transcription	Brain Substantia Nigra	brain
40	chr3:141174400-141175400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:141174400-141175400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
42	chr3:141174400-141176400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:141174400-141177600	Enhancers	K562	blood
44	chr3:141174600-141175000	Flanking Active TSS	NHLF	lung
45	chr3:141174600-141175200	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr3:141174600-141175400	Enhancers	Gastric	stomach
47	chr3:141174600-141176800	Enhancers	Stomach Mucosa	stomach
48	chr3:141174600-141178400	Enhancers	HepG2	liver
49	chr3:141174800-141175600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:141174800-141175600	Enhancers	Rectal Mucosa Donor 31	rectum

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