Variant report

Variant	rs57488435
Chromosome Location	chr6:56578146-56578147
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56572377..56575419-chr6:56576421..56579962,3	MCF-7	breast:
2	chr6:56577508..56579178-chr6:56607562..56609413,2	MCF-7	breast:
3	chr6:56567530..56570297-chr6:56577353..56579502,2	MCF-7	breast:

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1024196	1.00[ASN][1000 genomes]
rs11961141	0.89[ASN][1000 genomes]
rs11961342	1.00[ASN][1000 genomes]
rs11966986	1.00[ASN][1000 genomes]
rs11967796	1.00[ASN][1000 genomes]
rs11968575	0.89[ASN][1000 genomes]
rs11970410	0.90[ASN][1000 genomes]
rs13191164	1.00[ASN][1000 genomes]
rs13192478	0.89[ASN][1000 genomes]
rs13192567	0.89[ASN][1000 genomes]
rs13205013	1.00[ASN][1000 genomes]
rs13210876	0.89[ASN][1000 genomes]
rs13213878	0.89[ASN][1000 genomes]
rs13219546	0.89[ASN][1000 genomes]
rs16888085	0.90[ASN][1000 genomes]
rs16888096	1.00[ASN][1000 genomes]
rs16888106	1.00[ASN][1000 genomes]
rs16888118	1.00[ASN][1000 genomes]
rs16888124	1.00[ASN][1000 genomes]
rs16888128	1.00[ASN][1000 genomes]
rs16888130	1.00[ASN][1000 genomes]
rs16888133	1.00[ASN][1000 genomes]
rs16888135	0.89[ASN][1000 genomes]
rs2144407	1.00[ASN][1000 genomes]
rs2180148	1.00[ASN][1000 genomes]
rs2967960	0.89[ASN][1000 genomes]
rs3002003	0.89[ASN][1000 genomes]
rs3002004	0.89[ASN][1000 genomes]
rs34138864	0.90[ASN][1000 genomes]
rs34429594	1.00[ASN][1000 genomes]
rs34724718	1.00[ASN][1000 genomes]
rs34812826	0.89[ASN][1000 genomes]
rs34824960	0.89[ASN][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	1.00[ASN][1000 genomes]
rs35637749	1.00[ASN][1000 genomes]
rs35687635	1.00[ASN][1000 genomes]
rs35920751	0.89[ASN][1000 genomes]
rs36068365	1.00[ASN][1000 genomes]
rs4072271	1.00[ASN][1000 genomes]
rs41267673	1.00[ASN][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4275049	0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.89[ASN][1000 genomes]
rs56094263	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs57289287	1.00[ASN][1000 genomes]
rs57392123	1.00[ASN][1000 genomes]
rs58565063	1.00[ASN][1000 genomes]
rs59073430	1.00[ASN][1000 genomes]
rs59085778	0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.89[ASN][1000 genomes]
rs59772940	1.00[ASN][1000 genomes]
rs59889120	1.00[ASN][1000 genomes]
rs60360551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60498201	0.89[ASN][1000 genomes]
rs6459167	1.00[ASN][1000 genomes]
rs6459168	1.00[ASN][1000 genomes]
rs6900572	1.00[ASN][1000 genomes]
rs6901176	1.00[ASN][1000 genomes]
rs6903815	1.00[ASN][1000 genomes]
rs6916813	1.00[ASN][1000 genomes]
rs6924375	1.00[ASN][1000 genomes]
rs6926134	0.89[ASN][1000 genomes]
rs73746926	1.00[ASN][1000 genomes]
rs73746929	1.00[ASN][1000 genomes]
rs73746930	1.00[ASN][1000 genomes]
rs73746931	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7749100	1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7759479	1.00[ASN][1000 genomes]
rs7760503	1.00[ASN][1000 genomes]
rs7760542	1.00[ASN][1000 genomes]
rs7761027	1.00[ASN][1000 genomes]
rs7767128	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
2	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
3	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:56568000-56580400	Weak transcription	Brain Germinal Matrix	brain
5	chr6:56570000-56585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
7	chr6:56572400-56579400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr6:56574000-56579200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr6:56574800-56579800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:56574800-56580000	Weak transcription	Pancreas	Pancrea
11	chr6:56575200-56578200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:56575200-56578400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:56575800-56578400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:56576000-56579200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:56577200-56580800	Enhancers	Stomach Mucosa	stomach
16	chr6:56577200-56581200	Enhancers	HMEC	breast
17	chr6:56577200-56581400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:56577200-56581600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr6:56577400-56580000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr6:56577600-56579200	Enhancers	NHLF	lung
21	chr6:56577600-56579400	Enhancers	HSMMtube	muscle
22	chr6:56577600-56579400	Enhancers	Osteobl	bone
23	chr6:56577600-56579600	Enhancers	HUVEC	blood vessel
24	chr6:56577600-56580800	Enhancers	NHEK	skin
25	chr6:56577600-56581000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:56577600-56581400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:56577600-56581400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:56577600-56583000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:56577800-56578200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:56577800-56578200	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr6:56577800-56578200	Enhancers	Fetal Intestine Large	intestine
32	chr6:56577800-56578200	Enhancers	Fetal Intestine Small	intestine
33	chr6:56577800-56578200	Flanking Active TSS	HSMM	muscle
34	chr6:56577800-56578600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr6:56577800-56578600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr6:56577800-56578600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:56577800-56578600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:56577800-56578600	Enhancers	Ovary	ovary
39	chr6:56577800-56578800	Flanking Active TSS	A549	lung
40	chr6:56577800-56578800	Flanking Active TSS	NH-A	brain
41	chr6:56577800-56579000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr6:56577800-56579600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:56577800-56579600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:56577800-56580000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr6:56577800-56580000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:56577800-56580200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:56577800-56580800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr6:56577800-56580800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr6:56577800-56580800	Enhancers	Stomach Smooth Muscle	stomach
50	chr6:56577800-56581000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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