Variant report

Variant	rs3804381
Chromosome Location	chr4:102143616-102143617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102141797..102143717-chr4:102266068..102269227,3	MCF-7	breast:
2	chr4:102131746..102133996-chr4:102142309..102145275,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254531	Chromatin interaction
ENSG00000138814	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10004357	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10009468	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10009785	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10016548	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10016669	0.95[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10050301	0.82[CHB][hapmap]
rs10050344	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10516470	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1157038	0.84[YRI][hapmap]
rs11933861	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11934140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11937437	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11941610	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11941991	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11944013	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11946537	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13103487	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13112866	0.86[CHB][hapmap]
rs13115148	0.92[EUR][1000 genomes]
rs13115754	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13116679	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13117915	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13117949	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13123962	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13137393	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13151505	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1561721	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1837773	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2048072	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2135611	0.81[CHB][hapmap]
rs2135612	0.83[YRI][hapmap]
rs2165505	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583384	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2583405	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2583407	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28411074	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28478920	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2850335	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2850336	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850338	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2850350	0.82[JPT][hapmap]
rs2850359	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2850960	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2850961	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2850964	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2850971	0.95[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2850998	0.84[YRI][hapmap]
rs28513937	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28638776	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28698954	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35095772	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3789748	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804382	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804390	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3804393	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3804403	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3804404	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804406	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3804407	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804408	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3804409	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3804410	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3804416	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3804417	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3804420	0.86[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3804421	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3811063	0.81[CHB][hapmap]
rs3827771	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827773	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4413408	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4461528	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4525978	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4699139	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4699144	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4699163	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6532922	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6854591	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6854624	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs713454	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs713455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs750032	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs958379	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs962385	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs962386	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs970071	0.86[YRI][hapmap]
rs978373	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9997767	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[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:41 , 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	chr4:102133000-102143800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:102133000-102143800	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:102135800-102145200	Weak transcription	Small Intestine	intestine
5	chr4:102136000-102144400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:102136000-102145800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:102138400-102144800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:102139200-102144000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:102139200-102144000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr4:102139200-102145600	Weak transcription	Ovary	ovary
11	chr4:102139400-102152000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr4:102140000-102144600	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr4:102140200-102144400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:102140200-102146600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:102140400-102143800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:102140400-102144000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:102140400-102144200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:102140600-102144000	Weak transcription	Fetal Intestine Large	intestine
19	chr4:102142000-102144200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:102142000-102144400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:102142000-102153200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:102142200-102148000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:102142400-102144000	Enhancers	HSMM	muscle
24	chr4:102142600-102143800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:102142600-102144000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:102142600-102146000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:102142800-102144200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:102142800-102144400	Enhancers	HUVEC	blood vessel
29	chr4:102142800-102144400	Enhancers	Osteobl	bone
30	chr4:102142800-102144600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr4:102143000-102144000	Weak transcription	NHLF	lung
32	chr4:102143200-102143800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr4:102143400-102144200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:102143400-102144400	Enhancers	Fetal Heart	heart
35	chr4:102143400-102144400	Enhancers	Hela-S3	cervix
36	chr4:102143400-102144800	Enhancers	Adipose Nuclei	Adipose
37	chr4:102143400-102148800	Weak transcription	Primary B cells from cord blood	blood
38	chr4:102143600-102144000	Flanking Active TSS	A549	lung
39	chr4:102143600-102144200	Enhancers	NHDF-Ad	bronchial
40	chr4:102143600-102144400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr4:102143600-102144400	Enhancers	Stomach Mucosa	stomach

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