Variant report

Variant	rs5024547
Chromosome Location	chr6:56563093-56563094
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:56562960-56563110	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:56558539..56560309-chr6:56560912..56563103,2	MCF-7	breast:
2	chr6:56504038..56506002-chr6:56561278..56563980,2	MCF-7	breast:
3	chr6:56534855..56537779-chr6:56562012..56563518,2	MCF-7	breast:

Variant related genes	Relation type
DST	TF binding region

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

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

rs_ID	r²[population]
rs10498811	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[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	1.00[EUR][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192478	0.83[EUR][1000 genomes]
rs13192567	0.83[EUR][1000 genomes]
rs13196211	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[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	1.00[EUR][1000 genomes]
rs13206849	1.00[AFR][1000 genomes];1.00[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	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16888133	0.97[EUR][1000 genomes]
rs16888135	0.83[EUR][1000 genomes]
rs17684511	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684571	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17751682	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];0.98[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	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	1.00[AFR][1000 genomes];1.00[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35494794	0.85[EUR][1000 genomes]
rs35619924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35637749	1.00[EUR][1000 genomes]
rs35668437	0.98[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	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];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]
rs55742092	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56101897	0.98[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]
rs62412526	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412528	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62412556	0.83[EUR][1000 genomes]
rs6901176	1.00[EUR][1000 genomes]
rs6924375	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs6926134	0.83[EUR][1000 genomes]
rs6938003	0.82[EUR][1000 genomes]
rs71564848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71564849	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7767128	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr6:56549800-56578000	Weak transcription	Gastric	stomach
4	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr6:56555800-56573600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr6:56556000-56568400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:56556200-56573600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:56556400-56568000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:56558200-56563400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:56558200-56563600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:56558200-56569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:56558200-56573400	Weak transcription	Stomach Mucosa	stomach
15	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
16	chr6:56558400-56563400	Weak transcription	Brain Angular Gyrus	brain
17	chr6:56558400-56563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:56558400-56563600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:56558400-56566400	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:56558400-56567000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:56558400-56571600	Weak transcription	Fetal Stomach	stomach
22	chr6:56558400-56573200	Weak transcription	Adipose Nuclei	Adipose
23	chr6:56558400-56577800	Weak transcription	Ovary	ovary
24	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
25	chr6:56558600-56566400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
27	chr6:56559400-56563800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:56559600-56563200	Strong transcription	HSMM	muscle
29	chr6:56559600-56572600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:56559600-56573000	Weak transcription	NH-A	brain
31	chr6:56559800-56577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:56560400-56569800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:56560400-56577200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr6:56560600-56563600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr6:56560600-56572200	Weak transcription	NHDF-Ad	bronchial
37	chr6:56560600-56572400	Weak transcription	HMEC	breast
38	chr6:56561200-56563600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:56561200-56568400	Weak transcription	HUVEC	blood vessel
40	chr6:56561200-56571800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:56561400-56573200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:56561800-56564000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:56561800-56564000	Enhancers	Brain Substantia Nigra	brain
44	chr6:56561800-56564000	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr6:56561800-56565200	Strong transcription	GM12878-XiMat	blood
46	chr6:56562000-56569800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:56562000-56569800	Weak transcription	Left Ventricle	heart
48	chr6:56562000-56573200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:56562200-56563600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr6:56562200-56563800	Enhancers	Skeletal Muscle Male	skeletal muscle

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