Variant report

Variant	rs1013842
Chromosome Location	chr4:148783402-148783403
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	chr4:148603830..148606131-chr4:148782942..148784655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164169	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10004850	0.95[EUR][1000 genomes]
rs10007231	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10018820	0.86[JPT][hapmap]
rs10018903	0.86[JPT][hapmap]
rs10021936	0.99[EUR][1000 genomes]
rs10022691	0.99[EUR][1000 genomes]
rs10023057	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10025684	0.99[EUR][1000 genomes]
rs10030513	0.99[EUR][1000 genomes]
rs10461235	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11099670	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733409	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11737346	0.92[CEU][hapmap]
rs12498257	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511313	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129747	0.96[EUR][1000 genomes]
rs13148956	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13434396	0.99[EUR][1000 genomes]
rs1347596	0.89[EUR][1000 genomes]
rs1436489	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs1436490	0.91[EUR][1000 genomes]
rs1469865	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1469867	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17023928	0.86[JPT][hapmap]
rs17023995	0.83[CEU][hapmap];0.86[JPT][hapmap];0.99[EUR][1000 genomes]
rs28662484	0.91[EUR][1000 genomes]
rs35115631	0.96[EUR][1000 genomes]
rs35810358	0.82[AFR][1000 genomes]
rs4835101	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835461	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4835463	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4835464	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535565	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6839440	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6846526	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6846899	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6853296	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71616571	0.95[EUR][1000 genomes]
rs7654433	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7664567	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7666127	0.86[JPT][hapmap]
rs893024	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9996108	0.86[JPT][hapmap]

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	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148763200-148796200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:148764400-148786000	Weak transcription	NH-A	brain
3	chr4:148764400-148787000	Weak transcription	NHEK	skin
4	chr4:148764600-148787800	Weak transcription	HMEC	breast
5	chr4:148766400-148787600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:148766600-148796200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:148767600-148796400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr4:148768400-148815600	Weak transcription	Primary T cells from cord blood	blood
9	chr4:148770400-148796200	Weak transcription	Fetal Kidney	kidney
10	chr4:148772000-148806000	Weak transcription	Fetal Thymus	thymus
11	chr4:148772400-148785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr4:148776400-148787200	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:148777000-148796200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr4:148777000-148823000	Weak transcription	Small Intestine	intestine
15	chr4:148777200-148784400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:148777400-148796600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:148777800-148796200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:148778600-148787400	Weak transcription	Hela-S3	cervix
19	chr4:148779800-148793800	Weak transcription	Fetal Lung	lung
20	chr4:148780400-148784400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:148781200-148784200	Weak transcription	Osteobl	bone
22	chr4:148781600-148786400	Enhancers	Adipose Nuclei	Adipose
23	chr4:148782000-148783800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:148782000-148784000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr4:148782000-148799400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:148782200-148783600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:148782200-148783800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:148782200-148783800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr4:148782200-148783800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:148782200-148783800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
31	chr4:148782200-148783800	ZNF genes & repeats	Fetal Intestine Large	intestine
32	chr4:148782200-148783800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr4:148782200-148783800	Strong transcription	Fetal Stomach	stomach
34	chr4:148782200-148783800	Enhancers	Right Atrium	heart
35	chr4:148782400-148783600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:148782400-148784200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr4:148782400-148785400	Weak transcription	Spleen	Spleen
38	chr4:148782400-148786000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr4:148782600-148783800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:148782600-148784200	Weak transcription	Colonic Mucosa	Colon
41	chr4:148782600-148785000	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:148782800-148783800	Genic enhancers	Fetal Muscle Trunk	muscle
43	chr4:148782800-148786200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:148782800-148787800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr4:148783000-148783600	Strong transcription	Aorta	Aorta
46	chr4:148783000-148783600	Strong transcription	Fetal Intestine Small	intestine
47	chr4:148783000-148783800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:148783000-148783800	Enhancers	Right Ventricle	heart
49	chr4:148783000-148784000	Weak transcription	HUVEC	blood vessel
50	chr4:148783000-148784400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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