Variant report

Variant	rs34576803
Chromosome Location	chr6:56549407-56549408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10498811	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11961141	0.82[EUR][1000 genomes]
rs11961342	0.83[EUR][1000 genomes]
rs11968575	0.82[EUR][1000 genomes]
rs13191164	0.98[EUR][1000 genomes]
rs13192037	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13192478	0.82[EUR][1000 genomes]
rs13192567	0.82[EUR][1000 genomes]
rs13196211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13198399	0.82[EUR][1000 genomes]
rs13198938	0.82[EUR][1000 genomes]
rs13203000	0.81[EUR][1000 genomes]
rs13205013	0.98[EUR][1000 genomes]
rs13206849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13210876	0.81[EUR][1000 genomes]
rs13213878	0.81[EUR][1000 genomes]
rs13217390	0.81[EUR][1000 genomes]
rs13219546	0.81[EUR][1000 genomes]
rs13219942	0.83[EUR][1000 genomes]
rs16888118	0.98[EUR][1000 genomes]
rs16888124	0.98[EUR][1000 genomes]
rs16888126	0.95[EUR][1000 genomes]
rs16888128	0.97[EUR][1000 genomes]
rs16888130	0.97[EUR][1000 genomes]
rs16888133	0.95[EUR][1000 genomes]
rs16888135	0.81[EUR][1000 genomes]
rs17684511	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684553	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17684571	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17751682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17751695	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2967960	0.80[EUR][1000 genomes]
rs2967963	0.81[EUR][1000 genomes]
rs3002003	0.81[EUR][1000 genomes]
rs3002004	0.81[EUR][1000 genomes]
rs3002006	0.81[EUR][1000 genomes]
rs3002008	0.81[EUR][1000 genomes]
rs3002009	0.81[EUR][1000 genomes]
rs3002010	0.81[EUR][1000 genomes]
rs3002011	0.81[EUR][1000 genomes]
rs34138864	0.98[EUR][1000 genomes]
rs34429594	0.82[EUR][1000 genomes]
rs34455199	0.81[EUR][1000 genomes]
rs34465210	0.81[EUR][1000 genomes]
rs34566275	0.81[EUR][1000 genomes]
rs34587484	0.81[EUR][1000 genomes]
rs34623351	0.81[EUR][1000 genomes]
rs34724718	0.98[EUR][1000 genomes]
rs34803237	0.81[EUR][1000 genomes]
rs34812826	0.82[EUR][1000 genomes]
rs34824960	0.82[EUR][1000 genomes]
rs34832779	0.80[EUR][1000 genomes]
rs35206656	0.97[EUR][1000 genomes]
rs35326806	0.83[EUR][1000 genomes]
rs35408048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35494794	0.83[EUR][1000 genomes]
rs35619924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35637749	0.98[EUR][1000 genomes]
rs35668437	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35687635	0.97[EUR][1000 genomes]
rs35876418	0.81[EUR][1000 genomes]
rs35920751	0.82[EUR][1000 genomes]
rs36068365	0.83[EUR][1000 genomes]
rs4072271	0.97[EUR][1000 genomes]
rs4073960	0.96[EUR][1000 genomes]
rs4074101	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4074102	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4074103	0.95[EUR][1000 genomes]
rs41267675	0.81[EUR][1000 genomes]
rs4262190	0.89[EUR][1000 genomes]
rs4275049	0.81[EUR][1000 genomes]
rs4640889	0.81[EUR][1000 genomes]
rs5024547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55742092	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56101897	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59085778	0.82[EUR][1000 genomes]
rs59247267	0.81[EUR][1000 genomes]
rs60498201	0.81[EUR][1000 genomes]
rs62412526	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412528	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412531	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412556	0.81[EUR][1000 genomes]
rs6901176	0.98[EUR][1000 genomes]
rs6924375	0.98[EUR][1000 genomes]
rs6926134	0.82[EUR][1000 genomes]
rs6938003	0.80[EUR][1000 genomes]
rs71564848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71564849	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7767128	0.98[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:81 , 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	chr6:56529600-56553800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:56535200-56555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:56537000-56551800	Weak transcription	Esophagus	oesophagus
5	chr6:56537200-56553400	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:56537200-56555200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:56537600-56552600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:56537600-56553600	Weak transcription	Fetal Stomach	stomach
9	chr6:56543000-56559400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:56545600-56553400	Enhancers	Brain Hippocampus Middle	brain
11	chr6:56546200-56552400	Enhancers	Brain Substantia Nigra	brain
12	chr6:56546200-56564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:56546800-56555400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr6:56547000-56549800	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:56547200-56552200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr6:56547200-56552400	Enhancers	Brain Angular Gyrus	brain
17	chr6:56547200-56553400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:56547200-56554000	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:56547200-56557400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:56547400-56549600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr6:56547400-56549600	Enhancers	Colon Smooth Muscle	Colon
22	chr6:56547400-56552400	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr6:56547400-56552400	Enhancers	Ovary	ovary
24	chr6:56547400-56552800	Enhancers	Brain Anterior Caudate	brain
25	chr6:56547400-56561600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:56547600-56549600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:56547600-56550400	Enhancers	Fetal Lung	lung
28	chr6:56547800-56549600	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr6:56547800-56549800	Strong transcription	GM12878-XiMat	blood
30	chr6:56547800-56551800	Weak transcription	Right Ventricle	heart
31	chr6:56548000-56549600	Enhancers	Stomach Mucosa	stomach
32	chr6:56548000-56549600	Enhancers	HMEC	breast
33	chr6:56548000-56551000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:56548200-56549600	Enhancers	NHLF	lung
35	chr6:56548200-56549800	Enhancers	Fetal Intestine Large	intestine
36	chr6:56548200-56550000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:56548400-56549600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr6:56548400-56549600	Enhancers	NH-A	brain
39	chr6:56548600-56549600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:56548600-56549600	Enhancers	Colonic Mucosa	Colon
41	chr6:56548600-56549600	Enhancers	Duodenum Mucosa	Duodenum
42	chr6:56548600-56550400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr6:56548600-56550400	Enhancers	HSMM	muscle
44	chr6:56548600-56550600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:56548600-56552400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:56548800-56549600	Enhancers	HSMMtube	muscle
47	chr6:56548800-56549600	Enhancers	HUVEC	blood vessel
48	chr6:56548800-56549800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:56548800-56549800	Enhancers	Fetal Heart	heart
50	chr6:56548800-56549800	Enhancers	Osteobl	bone

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