Variant report

Variant	rs62412526
Chromosome Location	chr6:56553969-56553970
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56528704..56530414-chr6:56552846..56555109,2	MCF-7	breast:
2	chr6:56505033..56507671-chr6:56553691..56555258,2	MCF-7	breast:
3	chr6:56505646..56507890-chr6:56552731..56554323,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10498811	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11961141	0.83[EUR][1000 genomes]
rs11961342	0.85[EUR][1000 genomes]
rs11968575	0.83[EUR][1000 genomes]
rs13191164	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192037	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192478	0.83[EUR][1000 genomes]
rs13192567	0.83[EUR][1000 genomes]
rs13196211	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13198399	0.83[EUR][1000 genomes]
rs13198938	0.83[EUR][1000 genomes]
rs13203000	0.83[EUR][1000 genomes]
rs13205013	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13206849	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13210876	0.83[EUR][1000 genomes]
rs13213878	0.83[EUR][1000 genomes]
rs13217390	0.83[EUR][1000 genomes]
rs13219546	0.83[EUR][1000 genomes]
rs13219942	0.85[EUR][1000 genomes]
rs16888118	1.00[EUR][1000 genomes]
rs16888124	1.00[EUR][1000 genomes]
rs16888126	0.97[EUR][1000 genomes]
rs16888128	0.98[EUR][1000 genomes]
rs16888130	0.98[EUR][1000 genomes]
rs16888133	0.97[EUR][1000 genomes]
rs16888135	0.83[EUR][1000 genomes]
rs17684511	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684553	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684571	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17751682	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751695	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2967960	0.82[EUR][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.83[EUR][1000 genomes]
rs3002004	0.83[EUR][1000 genomes]
rs3002006	0.83[EUR][1000 genomes]
rs3002007	0.81[EUR][1000 genomes]
rs3002008	0.83[EUR][1000 genomes]
rs3002009	0.83[EUR][1000 genomes]
rs3002010	0.83[EUR][1000 genomes]
rs3002011	0.83[EUR][1000 genomes]
rs34138864	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34429594	0.84[EUR][1000 genomes]
rs34455199	0.83[EUR][1000 genomes]
rs34465210	0.83[EUR][1000 genomes]
rs34566275	0.83[EUR][1000 genomes]
rs34576803	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34587484	0.83[EUR][1000 genomes]
rs34623351	0.83[EUR][1000 genomes]
rs34724718	1.00[EUR][1000 genomes]
rs34803237	0.83[EUR][1000 genomes]
rs34812826	0.83[EUR][1000 genomes]
rs34824960	0.83[EUR][1000 genomes]
rs34832779	0.82[EUR][1000 genomes]
rs35206656	0.98[EUR][1000 genomes]
rs35326806	0.85[EUR][1000 genomes]
rs35408048	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35494794	0.85[EUR][1000 genomes]
rs35619924	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35637749	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35668437	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35687635	0.98[EUR][1000 genomes]
rs35876418	0.83[EUR][1000 genomes]
rs35920751	0.83[EUR][1000 genomes]
rs36068365	0.85[EUR][1000 genomes]
rs4072271	0.98[EUR][1000 genomes]
rs4073960	0.95[EUR][1000 genomes]
rs4074101	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074102	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074103	0.97[EUR][1000 genomes]
rs41267675	0.83[EUR][1000 genomes]
rs4262190	0.91[EUR][1000 genomes]
rs4275049	0.83[EUR][1000 genomes]
rs4640889	0.83[EUR][1000 genomes]
rs5024547	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55742092	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56101897	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59085778	0.83[EUR][1000 genomes]
rs59247267	0.83[EUR][1000 genomes]
rs60498201	0.83[EUR][1000 genomes]
rs62412528	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412531	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412532	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412556	0.83[EUR][1000 genomes]
rs6901176	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6924375	1.00[EUR][1000 genomes]
rs6926134	0.83[EUR][1000 genomes]
rs6938003	0.82[EUR][1000 genomes]
rs71564848	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564849	0.98[EUR][1000 genomes]
rs7767128	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv432888	chr6:56507489-56560764	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56527000-56554400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:56535200-56555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:56537200-56555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:56543000-56559400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:56546800-56555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr6:56547200-56554000	Enhancers	Brain Cingulate Gyrus	brain
8	chr6:56547200-56557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:56548800-56554000	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:56549600-56554200	Weak transcription	NH-A	brain
12	chr6:56549600-56554400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:56549600-56554600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:56549600-56554600	Weak transcription	HUVEC	blood vessel
15	chr6:56549600-56558000	Weak transcription	HMEC	breast
16	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:56549800-56554200	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:56549800-56555200	Weak transcription	Fetal Heart	heart
19	chr6:56549800-56555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:56549800-56578000	Weak transcription	Gastric	stomach
21	chr6:56550400-56554400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr6:56550400-56555400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:56550600-56555200	Genic enhancers	HSMM	muscle
24	chr6:56550800-56554800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:56551600-56554000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:56552000-56554600	Weak transcription	Left Ventricle	heart
27	chr6:56552200-56557200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:56552400-56554400	Weak transcription	Ovary	ovary
29	chr6:56552800-56554000	Weak transcription	Stomach Mucosa	stomach
30	chr6:56553000-56554000	Flanking Active TSS	Fetal Lung	lung
31	chr6:56553200-56554800	Genic enhancers	NHDF-Ad	bronchial
32	chr6:56553200-56555400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:56553200-56558600	Active TSS	Fetal Intestine Large	intestine
34	chr6:56553200-56558600	Active TSS	Fetal Intestine Small	intestine
35	chr6:56553400-56554000	Enhancers	GM12878-XiMat	blood
36	chr6:56553400-56554000	Enhancers	NHEK	skin
37	chr6:56553400-56554200	Enhancers	Brain Angular Gyrus	brain
38	chr6:56553400-56554200	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr6:56553400-56554600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr6:56553400-56554800	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr6:56553400-56555000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:56553400-56555000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr6:56553400-56555200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:56553400-56555200	Enhancers	Hela-S3	cervix
45	chr6:56553400-56555800	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr6:56553400-56556000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:56553400-56556400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:56553400-56557200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:56553400-56557400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:56553400-56558400	Active TSS	Right Ventricle	heart

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