Variant report

Variant	rs13213878
Chromosome Location	chr6:56589841-56589842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56589671..56592366-chr6:56593066..56595730,2	MCF-7	breast:
2	chr6:56588457..56590419-chr6:56592113..56594629,2	K562	blood:

Extended variants
information (count: 146 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs1024196	0.89[ASN][1000 genomes]
rs10498811	0.83[EUR][1000 genomes]
rs11961141	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11961342	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11966986	0.89[ASN][1000 genomes]
rs11967796	0.89[ASN][1000 genomes]
rs11968575	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11970648	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13191164	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192567	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196211	0.81[EUR][1000 genomes]
rs13198399	0.99[EUR][1000 genomes]
rs13198938	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13203000	0.98[EUR][1000 genomes]
rs13205013	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13206849	0.83[EUR][1000 genomes]
rs13208409	0.80[EUR][1000 genomes]
rs13210876	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13217390	0.98[EUR][1000 genomes]
rs13219546	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219942	0.97[EUR][1000 genomes]
rs16888070	0.89[ASN][1000 genomes]
rs16888096	0.89[ASN][1000 genomes]
rs16888106	0.89[ASN][1000 genomes]
rs16888118	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888124	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888126	0.80[EUR][1000 genomes]
rs16888128	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888130	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888133	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888135	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.84[EUR][1000 genomes]
rs17684571	0.84[EUR][1000 genomes]
rs17751682	0.83[EUR][1000 genomes]
rs17751695	0.83[EUR][1000 genomes]
rs2144407	0.89[ASN][1000 genomes]
rs2180148	0.89[ASN][1000 genomes]
rs2207678	0.89[ASN][1000 genomes]
rs2967960	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967963	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002003	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002004	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002006	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002007	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002008	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002009	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002010	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002011	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34429594	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34455199	0.98[EUR][1000 genomes]
rs34463732	0.91[EUR][1000 genomes]
rs34465210	0.98[EUR][1000 genomes]
rs34566275	0.98[EUR][1000 genomes]
rs34576803	0.81[EUR][1000 genomes]
rs34587484	0.98[EUR][1000 genomes]
rs34623351	0.98[EUR][1000 genomes]
rs34703847	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34724718	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34803237	0.98[EUR][1000 genomes]
rs34812826	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34824960	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832779	0.97[EUR][1000 genomes]
rs35089136	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35206656	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35326806	0.97[EUR][1000 genomes]
rs35408048	0.83[EUR][1000 genomes]
rs35494794	0.97[EUR][1000 genomes]
rs35619924	0.83[EUR][1000 genomes]
rs35637749	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35668437	0.83[EUR][1000 genomes]
rs35687635	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35876418	0.98[EUR][1000 genomes]
rs35920751	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36068365	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4072271	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073960	0.82[AFR][1000 genomes]
rs4074101	0.83[EUR][1000 genomes]
rs4074102	0.83[EUR][1000 genomes]
rs4074103	0.80[EUR][1000 genomes]
rs41267673	0.89[ASN][1000 genomes]
rs41267675	0.98[EUR][1000 genomes]
rs41271876	0.89[ASN][1000 genomes]
rs41271878	0.89[ASN][1000 genomes]
rs4133076	0.89[ASN][1000 genomes]
rs4275049	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45553042	0.89[ASN][1000 genomes]
rs4574644	1.00[ASN][1000 genomes]
rs4640889	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56094263	1.00[ASN][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs56196625	0.89[ASN][1000 genomes]
rs57289287	0.89[ASN][1000 genomes]
rs57350484	0.89[ASN][1000 genomes]
rs57392123	0.89[ASN][1000 genomes]
rs57488435	0.89[ASN][1000 genomes]
rs58565063	0.89[ASN][1000 genomes]
rs59073430	0.89[ASN][1000 genomes]
rs59085778	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59162324	1.00[ASN][1000 genomes]
rs59247267	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59772940	0.89[ASN][1000 genomes]
rs59889120	0.89[ASN][1000 genomes]
rs60360551	0.89[ASN][1000 genomes]
rs60498201	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62412526	0.83[EUR][1000 genomes]
rs62412528	0.83[EUR][1000 genomes]
rs62412531	0.83[EUR][1000 genomes]
rs62412532	0.83[EUR][1000 genomes]
rs62412544	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62412556	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6459167	0.89[ASN][1000 genomes]
rs6459168	0.89[ASN][1000 genomes]
rs6900572	0.89[ASN][1000 genomes]
rs6901176	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6903815	0.89[ASN][1000 genomes]
rs6904535	0.81[AMR][1000 genomes]
rs6916813	0.89[ASN][1000 genomes]
rs6924375	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926134	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938003	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6941626	0.89[ASN][1000 genomes]
rs71564848	0.81[EUR][1000 genomes]
rs71564849	0.84[EUR][1000 genomes]
rs73746926	0.89[ASN][1000 genomes]
rs73746929	0.89[ASN][1000 genomes]
rs73746930	0.89[ASN][1000 genomes]
rs73746931	0.89[ASN][1000 genomes]
rs7749100	0.89[ASN][1000 genomes]
rs7749437	0.89[ASN][1000 genomes]
rs7759479	0.89[ASN][1000 genomes]
rs7760503	0.89[ASN][1000 genomes]
rs7760542	0.89[ASN][1000 genomes]
rs7761027	0.89[ASN][1000 genomes]
rs7767128	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7775134	0.89[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:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
2	chr6:56579400-56592000	Weak transcription	Lung	lung
3	chr6:56580800-56592000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr6:56580800-56595800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:56581000-56590000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr6:56581200-56590200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:56581400-56592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:56581600-56597800	Weak transcription	Fetal Brain Male	brain
9	chr6:56582600-56611600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:56583600-56591200	Weak transcription	NHEK	skin
11	chr6:56583800-56590800	Weak transcription	HMEC	breast
12	chr6:56584600-56593600	Weak transcription	HUVEC	blood vessel
13	chr6:56584800-56599800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:56586000-56590000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr6:56586200-56590000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:56586400-56595600	Weak transcription	Adipose Nuclei	Adipose
17	chr6:56586800-56592000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:56586800-56593600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:56587200-56591000	Weak transcription	GM12878-XiMat	blood
20	chr6:56587400-56596200	Enhancers	Stomach Mucosa	stomach
21	chr6:56588000-56590400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:56588400-56592000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:56588400-56598000	Enhancers	Osteobl	bone
24	chr6:56588600-56590200	Enhancers	Brain Anterior Caudate	brain
25	chr6:56588600-56590200	Enhancers	Stomach Smooth Muscle	stomach
26	chr6:56588600-56590400	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:56588600-56590400	Enhancers	Brain Substantia Nigra	brain
28	chr6:56588600-56590400	Enhancers	Psoas Muscle	Psoas
29	chr6:56588600-56590400	Genic enhancers	HSMM	muscle
30	chr6:56588600-56590400	Enhancers	NH-A	brain
31	chr6:56588600-56590600	Enhancers	Colon Smooth Muscle	Colon
32	chr6:56588600-56591200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:56588600-56592200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr6:56588600-56595200	Enhancers	Fetal Intestine Small	intestine
35	chr6:56588600-56596200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:56588800-56590600	Enhancers	Brain Hippocampus Middle	brain
37	chr6:56588800-56590800	Enhancers	NHDF-Ad	bronchial
38	chr6:56588800-56591000	Weak transcription	Placenta	Placenta
39	chr6:56588800-56591600	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:56588800-56592600	Enhancers	HepG2	liver
41	chr6:56588800-56593200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr6:56588800-56594600	Enhancers	A549	lung
43	chr6:56588800-56595800	Weak transcription	Left Ventricle	heart
44	chr6:56588800-56603400	Weak transcription	Right Ventricle	heart
45	chr6:56589000-56590000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:56589000-56590400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:56589000-56590400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr6:56589000-56590400	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:56589000-56593200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr6:56589200-56590200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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