Variant report

Variant	rs34623351
Chromosome Location	chr6:56614077-56614078
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56613706..56615863-chr6:56618976..56621667,2	K562	blood:
2	chr12:121788754..121791153-chr6:56613392..56614982,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000089053	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10498811	0.83[EUR][1000 genomes]
rs10498812	0.83[AFR][1000 genomes]
rs11756551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11961141	0.99[EUR][1000 genomes]
rs11961342	0.97[EUR][1000 genomes]
rs11968575	0.99[EUR][1000 genomes]
rs11970648	0.90[EUR][1000 genomes]
rs13191164	0.83[EUR][1000 genomes]
rs13192037	0.83[EUR][1000 genomes]
rs13192478	0.99[EUR][1000 genomes]
rs13192567	0.99[EUR][1000 genomes]
rs13194904	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13195601	0.83[AFR][1000 genomes]
rs13196211	0.82[EUR][1000 genomes]
rs13198204	0.84[AMR][1000 genomes]
rs13198399	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13198938	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13200166	0.84[AMR][1000 genomes]
rs13200559	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs13200768	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13200868	0.85[AMR][1000 genomes]
rs13201639	0.84[AMR][1000 genomes]
rs13201733	0.84[AMR][1000 genomes]
rs13203000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13203148	0.83[AFR][1000 genomes]
rs13203327	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13204466	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs13205013	0.83[EUR][1000 genomes]
rs13205667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs13206849	0.83[EUR][1000 genomes]
rs13208409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13210876	1.00[EUR][1000 genomes]
rs13211879	0.83[AFR][1000 genomes]
rs13213878	0.98[EUR][1000 genomes]
rs13217390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13218913	0.84[AMR][1000 genomes]
rs13219546	1.00[EUR][1000 genomes]
rs13219942	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13220851	0.84[AMR][1000 genomes]
rs16888118	0.83[EUR][1000 genomes]
rs16888124	0.83[EUR][1000 genomes]
rs16888126	0.80[EUR][1000 genomes]
rs16888128	0.84[EUR][1000 genomes]
rs16888130	0.84[EUR][1000 genomes]
rs16888133	0.82[EUR][1000 genomes]
rs16888135	1.00[EUR][1000 genomes]
rs17684511	0.83[EUR][1000 genomes]
rs17684553	0.84[EUR][1000 genomes]
rs17684571	0.84[EUR][1000 genomes]
rs17684730	0.84[AMR][1000 genomes]
rs17684748	0.84[AMR][1000 genomes]
rs17684772	0.84[AMR][1000 genomes]
rs17684784	0.82[AMR][1000 genomes]
rs17684802	0.84[AMR][1000 genomes]
rs17751682	0.83[EUR][1000 genomes]
rs17751695	0.83[EUR][1000 genomes]
rs17751966	0.84[AMR][1000 genomes]
rs17751977	0.84[AMR][1000 genomes]
rs17752002	0.84[AMR][1000 genomes]
rs17752046	0.84[AMR][1000 genomes]
rs2967960	0.99[EUR][1000 genomes]
rs2967963	0.98[EUR][1000 genomes]
rs3002003	1.00[EUR][1000 genomes]
rs3002004	1.00[EUR][1000 genomes]
rs3002006	1.00[EUR][1000 genomes]
rs3002007	0.98[EUR][1000 genomes]
rs3002008	1.00[EUR][1000 genomes]
rs3002009	1.00[EUR][1000 genomes]
rs3002010	1.00[EUR][1000 genomes]
rs3002011	1.00[EUR][1000 genomes]
rs34138864	0.83[EUR][1000 genomes]
rs34171958	0.84[AMR][1000 genomes]
rs34228698	0.84[AMR][1000 genomes]
rs34425815	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34429594	0.97[EUR][1000 genomes]
rs34455199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34463732	0.91[EUR][1000 genomes]
rs34465210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34500949	0.85[AMR][1000 genomes]
rs34566275	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34576803	0.81[EUR][1000 genomes]
rs34587484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34612783	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34640766	0.84[AMR][1000 genomes]
rs34703847	0.93[EUR][1000 genomes]
rs34724718	0.83[EUR][1000 genomes]
rs34803237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34812826	0.99[EUR][1000 genomes]
rs34824960	0.99[EUR][1000 genomes]
rs34832779	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34866877	0.83[AFR][1000 genomes]
rs34966024	0.89[AMR][1000 genomes]
rs35089136	0.80[EUR][1000 genomes]
rs35206656	0.84[EUR][1000 genomes]
rs35225175	0.83[AFR][1000 genomes]
rs35251663	0.84[AMR][1000 genomes]
rs35326806	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35407078	0.83[AFR][1000 genomes]
rs35408048	0.83[EUR][1000 genomes]
rs35439100	0.83[AFR][1000 genomes]
rs35440822	0.84[AMR][1000 genomes]
rs35494794	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35566812	0.84[AMR][1000 genomes]
rs35619924	0.83[EUR][1000 genomes]
rs35637749	0.83[EUR][1000 genomes]
rs35668437	0.83[EUR][1000 genomes]
rs35687635	0.84[EUR][1000 genomes]
rs35696739	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35828379	0.83[AFR][1000 genomes]
rs35873865	0.93[AMR][1000 genomes]
rs35876418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35920751	0.99[EUR][1000 genomes]
rs35986172	0.89[AMR][1000 genomes]
rs36037734	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs36068365	0.97[EUR][1000 genomes]
rs4072271	0.84[EUR][1000 genomes]
rs4074101	0.83[EUR][1000 genomes]
rs4074102	0.83[EUR][1000 genomes]
rs4074103	0.80[EUR][1000 genomes]
rs41267675	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4275049	1.00[EUR][1000 genomes]
rs4299824	0.84[AMR][1000 genomes]
rs4348308	0.84[AMR][1000 genomes]
rs4371846	0.84[AMR][1000 genomes]
rs4457154	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4640889	1.00[EUR][1000 genomes]
rs5024547	0.83[EUR][1000 genomes]
rs55742092	0.82[EUR][1000 genomes]
rs56101897	0.83[EUR][1000 genomes]
rs56368885	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs58980183	0.81[AMR][1000 genomes]
rs59085778	0.99[EUR][1000 genomes]
rs59247267	1.00[EUR][1000 genomes]
rs59432342	0.81[AMR][1000 genomes]
rs60498201	0.98[EUR][1000 genomes]
rs62411366	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs62411367	0.98[AMR][1000 genomes]
rs62411372	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs62411375	0.81[AMR][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	0.91[EUR][1000 genomes]
rs62412556	0.98[EUR][1000 genomes]
rs6901176	0.83[EUR][1000 genomes]
rs6924375	0.83[EUR][1000 genomes]
rs6926134	0.99[EUR][1000 genomes]
rs6928104	0.98[AMR][1000 genomes]
rs6938003	0.99[EUR][1000 genomes]
rs71564848	0.81[EUR][1000 genomes]
rs71564849	0.84[EUR][1000 genomes]
rs71564854	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs71564855	0.84[AMR][1000 genomes]
rs71564856	0.84[AMR][1000 genomes]
rs71564861	0.84[AMR][1000 genomes]
rs7767128	0.83[EUR][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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56593200-56621200	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:56605600-56614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:56606600-56617600	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr6:56607200-56614200	Weak transcription	Gastric	stomach
5	chr6:56607200-56618200	Weak transcription	Brain Germinal Matrix	brain
6	chr6:56607600-56620600	Weak transcription	Fetal Intestine Small	intestine
7	chr6:56608200-56614600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:56608200-56621000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:56608400-56614200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:56608400-56614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:56608600-56614400	Weak transcription	NHDF-Ad	bronchial
12	chr6:56608600-56618000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:56609200-56617600	Enhancers	HMEC	breast
14	chr6:56609200-56619200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:56609800-56614800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:56610000-56614200	Weak transcription	NHLF	lung
17	chr6:56610600-56614200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr6:56611600-56625800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:56611800-56614600	Weak transcription	Esophagus	oesophagus
20	chr6:56611800-56616200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:56612000-56614600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr6:56612000-56614600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:56612000-56616400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:56612200-56614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:56612200-56614200	Weak transcription	GM12878-XiMat	blood
26	chr6:56612200-56614400	Weak transcription	Brain Hippocampus Middle	brain
27	chr6:56612200-56614400	Weak transcription	HSMMtube	muscle
28	chr6:56612200-56614600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:56612200-56614600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:56612200-56614600	Weak transcription	Brain Angular Gyrus	brain
31	chr6:56612200-56614600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:56612200-56614600	Weak transcription	Fetal Heart	heart
33	chr6:56612200-56614600	Weak transcription	Right Atrium	heart
34	chr6:56612200-56616200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:56612200-56616600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:56612200-56616600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:56612200-56620800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:56612400-56614200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:56612400-56614200	Weak transcription	Osteobl	bone
40	chr6:56612400-56614600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:56612400-56614600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr6:56612400-56614600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:56612400-56614600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:56612400-56614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr6:56612400-56616800	Weak transcription	Brain Substantia Nigra	brain
46	chr6:56612400-56621800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:56612600-56614200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:56612600-56615600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:56613000-56614600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr6:56613000-56617400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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