Variant report

Variant	rs62486990
Chromosome Location	chr7:105178005-105178006
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:105174875..105178422-chr7:105279003..105282206,4	MCF-7	breast:
2	chr7:105171433..105173431-chr7:105176535..105180358,4	MCF-7	breast:
3	chr7:105161026..105164361-chr7:105174474..105178643,4	MCF-7	breast:
4	chr7:105171303..105174411-chr7:105176077..105181251,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135249	Chromatin interaction
ENSG00000091127	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs12538052	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540022	0.90[EUR][1000 genomes]
rs1728646	0.87[EUR][1000 genomes]
rs2463632	0.95[EUR][1000 genomes]
rs2463634	0.85[EUR][1000 genomes]
rs2692428	0.88[EUR][1000 genomes]
rs3735368	0.81[ASN][1000 genomes]
rs4373450	0.81[ASN][1000 genomes]
rs4585682	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55650695	0.81[ASN][1000 genomes]
rs55807006	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62486981	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486982	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62486983	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486984	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62486989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62486991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486992	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62486996	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62486997	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62486998	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62487001	0.89[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960696	0.81[ASN][1000 genomes]
rs6964788	0.81[ASN][1000 genomes]
rs6971072	0.81[ASN][1000 genomes]
rs698191	0.88[EUR][1000 genomes]
rs711435	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73190117	0.81[ASN][1000 genomes]
rs73190120	0.81[ASN][1000 genomes]
rs7790660	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7790913	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798871	0.81[ASN][1000 genomes]
rs818479	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs818625	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757233	chr7:104758250-105208492	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2759549	chr7:104758250-105208492	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1028228	chr7:104807207-105182998	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1015688	chr7:104849770-105182998	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1023767	chr7:104931143-105190662	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv539049	chr7:104931143-105190662	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv1022065	chr7:104997315-105190662	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv888932	chr7:105012975-105179756	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv888933	chr7:105012975-105193051	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv1023564	chr7:105018484-105182998	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv464668	chr7:105088693-105208492	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
12	nsv608069	chr7:105088693-105208492	Weak transcription Strong transcription Flanking Active TSS 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 miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv888935	chr7:105110990-105193051	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	30 gene(s)	inside rSNPs	diseases
14	nsv888936	chr7:105119308-105193051	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:105173400-105190200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:105173400-105208200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:105173400-105210200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:105173800-105178400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:105173800-105179000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:105173800-105183200	Weak transcription	Fetal Brain Male	brain
7	chr7:105174000-105178800	Weak transcription	Brain Anterior Caudate	brain
8	chr7:105174000-105204200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:105174000-105210200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:105174000-105212200	Weak transcription	Fetal Heart	heart
11	chr7:105174200-105178400	Weak transcription	Adipose Nuclei	Adipose
12	chr7:105174200-105178400	Weak transcription	Ovary	ovary
13	chr7:105174200-105178400	Weak transcription	Spleen	Spleen
14	chr7:105174200-105178600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:105174200-105178800	Weak transcription	Fetal Kidney	kidney
16	chr7:105174200-105178800	Weak transcription	Right Ventricle	heart
17	chr7:105174200-105178800	Weak transcription	HMEC	breast
18	chr7:105174200-105178800	Weak transcription	NHLF	lung
19	chr7:105174200-105179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:105174200-105210200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:105174200-105213800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr7:105174400-105178200	Weak transcription	Brain Angular Gyrus	brain
23	chr7:105174400-105178800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:105174400-105180200	Strong transcription	HSMM	muscle
25	chr7:105174600-105178400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr7:105174600-105178400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:105174600-105178600	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:105174600-105178800	Weak transcription	HepG2	liver
29	chr7:105174600-105180600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr7:105174600-105181600	Weak transcription	Hela-S3	cervix
31	chr7:105174600-105182800	Weak transcription	Small Intestine	intestine
32	chr7:105174600-105193400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:105174600-105210400	Weak transcription	Psoas Muscle	Psoas
34	chr7:105174600-105213200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:105174800-105178200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr7:105174800-105178200	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr7:105174800-105178800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:105174800-105185200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr7:105174800-105193800	Strong transcription	K562	blood
40	chr7:105174800-105209200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:105175000-105193000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:105175000-105210400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:105175200-105187400	Weak transcription	Stomach Mucosa	stomach
44	chr7:105175200-105194000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:105175400-105184800	Strong transcription	Osteobl	bone
46	chr7:105175400-105193000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:105175400-105193800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr7:105175400-105201200	Strong transcription	Primary B cells from peripheral blood	blood
49	chr7:105175400-105211000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:105175600-105196800	Strong transcription	Fetal Stomach	stomach

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