Variant report

Variant	rs3804382
Chromosome Location	chr4:102144751-102144752
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102131746..102133996-chr4:102142309..102145275,2	MCF-7	breast:
2	chr4:102143700..102146014-chr4:102149616..102151234,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10004357	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10009468	0.93[EUR][1000 genomes]
rs10009785	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10016548	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10016669	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10050344	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10516470	0.91[EUR][1000 genomes]
rs11933861	0.93[EUR][1000 genomes]
rs11934140	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11937437	0.91[EUR][1000 genomes]
rs11941610	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11941991	0.86[EUR][1000 genomes]
rs11944013	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11946537	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13103487	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13115148	0.91[EUR][1000 genomes]
rs13115754	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13116679	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13117915	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13117949	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13123962	0.93[EUR][1000 genomes]
rs13137393	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13151505	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1561721	0.91[EUR][1000 genomes]
rs1837773	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2165505	0.93[EUR][1000 genomes]
rs2583384	0.89[EUR][1000 genomes]
rs2583405	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2583407	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28411074	0.91[EUR][1000 genomes]
rs28478920	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2850335	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850336	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850338	0.93[EUR][1000 genomes]
rs2850359	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850960	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850961	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2850964	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2850971	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28513937	0.84[EUR][1000 genomes]
rs28638776	0.91[EUR][1000 genomes]
rs28698954	0.91[EUR][1000 genomes]
rs35095772	0.90[EUR][1000 genomes]
rs3789748	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804381	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804390	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3804393	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804403	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804404	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804406	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3804407	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804408	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3804409	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804410	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3804416	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804417	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3804420	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3804421	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3827771	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3827773	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4413408	0.93[EUR][1000 genomes]
rs4461528	0.93[EUR][1000 genomes]
rs4525978	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4699139	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4699144	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4699163	0.93[EUR][1000 genomes]
rs60154086	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6532922	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6854591	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6854624	0.92[EUR][1000 genomes]
rs713454	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs713455	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs750032	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs925028	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs958379	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs962385	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs962386	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs978373	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9997767	0.99[EUR][1000 genomes];0.82[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	nsv931418	chr4:101500167-102443207	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv999741	chr4:102009017-102454115	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537199	chr4:102009017-102454115	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1004766	chr4:102009017-102713765	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537200	chr4:102009017-102713765	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1011351	chr4:102056024-102450302	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102131800-102146000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:102135800-102145200	Weak transcription	Small Intestine	intestine
3	chr4:102136000-102145800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr4:102138400-102144800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:102139200-102145600	Weak transcription	Ovary	ovary
6	chr4:102139400-102152000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:102140200-102146600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:102142000-102153200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:102142200-102148000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:102142600-102146000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:102143400-102144800	Enhancers	Adipose Nuclei	Adipose
12	chr4:102143400-102148800	Weak transcription	Primary B cells from cord blood	blood
13	chr4:102143800-102144800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:102143800-102144800	Enhancers	Brain Anterior Caudate	brain
15	chr4:102143800-102146000	Enhancers	Colon Smooth Muscle	Colon
16	chr4:102144000-102144800	Enhancers	NHLF	lung
17	chr4:102144000-102145600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr4:102144000-102146000	Weak transcription	HSMM	muscle
19	chr4:102144000-102146600	Enhancers	A549	lung
20	chr4:102144000-102147400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:102144000-102148800	Weak transcription	HMEC	breast
22	chr4:102144200-102150000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:102144200-102150800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:102144400-102145200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr4:102144400-102145200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:102144400-102145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:102144400-102147400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:102144400-102147400	Weak transcription	NHEK	skin
29	chr4:102144600-102145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:102144600-102145400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr4:102144600-102145400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr4:102144600-102151800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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