Variant report

Variant	rs56196625
Chromosome Location	chr6:56579903-56579904
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56579501..56581287-chr6:56582321..56583913,2	MCF-7	breast:
2	chr6:56572377..56575419-chr6:56576421..56579962,3	MCF-7	breast:
3	chr6:56578404..56582346-chr6:56590205..56594810,5	MCF-7	breast:
4	chr6:56578880..56580854-chr6:56591144..56593853,2	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	0.89[ASN][1000 genomes]
rs57289287	1.00[ASN][1000 genomes]
rs57392123	1.00[ASN][1000 genomes]
rs57488435	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[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	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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56568000-56580400	Weak transcription	Brain Germinal Matrix	brain
2	chr6:56570000-56585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
4	chr6:56574800-56580000	Weak transcription	Pancreas	Pancrea
5	chr6:56577200-56580800	Enhancers	Stomach Mucosa	stomach
6	chr6:56577200-56581200	Enhancers	HMEC	breast
7	chr6:56577200-56581400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:56577200-56581600	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr6:56577400-56580000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:56577600-56580800	Enhancers	NHEK	skin
11	chr6:56577600-56581000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:56577600-56581400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:56577600-56581400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr6:56577600-56583000	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr6:56577800-56580000	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:56577800-56580000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:56577800-56580200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:56577800-56580800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr6:56577800-56580800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:56577800-56580800	Enhancers	Stomach Smooth Muscle	stomach
21	chr6:56577800-56581000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:56577800-56581000	Enhancers	Liver	Liver
23	chr6:56577800-56581000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:56577800-56581200	Enhancers	Fetal Heart	heart
25	chr6:56577800-56581200	Enhancers	HepG2	liver
26	chr6:56577800-56581400	Enhancers	Brain Angular Gyrus	brain
27	chr6:56577800-56581400	Enhancers	Colon Smooth Muscle	Colon
28	chr6:56577800-56581400	Enhancers	Rectal Smooth Muscle	rectum
29	chr6:56577800-56581400	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:56577800-56581600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:56577800-56581600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:56577800-56581600	Enhancers	Brain Anterior Caudate	brain
33	chr6:56577800-56581600	Enhancers	Brain Cingulate Gyrus	brain
34	chr6:56577800-56581600	Enhancers	Brain Hippocampus Middle	brain
35	chr6:56577800-56581600	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr6:56577800-56581600	Enhancers	Brain Substantia Nigra	brain
37	chr6:56577800-56581600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr6:56577800-56582600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:56577800-56582800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:56577800-56582800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:56577800-56583600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:56578000-56580400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:56578000-56580400	Enhancers	Gastric	stomach
44	chr6:56578000-56580600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr6:56578000-56580800	Enhancers	Left Ventricle	heart
46	chr6:56578000-56581600	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr6:56578000-56581600	Enhancers	Psoas Muscle	Psoas
48	chr6:56578200-56580000	Weak transcription	Fetal Intestine Small	intestine
49	chr6:56578200-56581600	Enhancers	HSMM	muscle
50	chr6:56578400-56581200	Enhancers	GM12878-XiMat	blood

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