Variant report

Variant	rs3924307
Chromosome Location	chr6:56377026-56377027
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56376171..56378986-chr6:56407329..56410206,2	K562	blood:
2	chr6:56376106..56377836-chr6:56404859..56408896,4	K562	blood:
3	chr6:56371302..56373415-chr6:56374644..56377108,2	K562	blood:
4	chr6:56376128..56377836-chr6:56405249..56407124,2	K562	blood:
5	chr6:56374485..56377341-chr6:56380470..56384676,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1024196	0.94[EUR][1000 genomes]
rs11963288	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11966986	0.94[EUR][1000 genomes]
rs11967796	0.94[EUR][1000 genomes]
rs11970410	0.94[EUR][1000 genomes]
rs1407831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1535609	1.00[EUR][1000 genomes]
rs1535611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16887928	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16888070	0.94[EUR][1000 genomes]
rs16888106	0.94[EUR][1000 genomes]
rs2144407	0.94[EUR][1000 genomes]
rs2180148	0.94[EUR][1000 genomes]
rs2207678	0.94[EUR][1000 genomes]
rs2397224	0.94[EUR][1000 genomes]
rs28633631	0.94[EUR][1000 genomes]
rs3800026	1.00[EUR][1000 genomes]
rs41267673	0.94[EUR][1000 genomes]
rs41271848	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41271850	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41271854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41271856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41271872	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs41271876	0.94[EUR][1000 genomes]
rs41271878	0.94[EUR][1000 genomes]
rs4256439	1.00[EUR][1000 genomes]
rs4288197	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs45442999	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs45553042	0.89[EUR][1000 genomes]
rs57289287	0.94[EUR][1000 genomes]
rs57350484	0.94[EUR][1000 genomes]
rs57790896	0.94[EUR][1000 genomes]
rs57822928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58565063	0.94[EUR][1000 genomes]
rs58730144	1.00[EUR][1000 genomes]
rs59772940	0.94[EUR][1000 genomes]
rs59864125	1.00[EUR][1000 genomes]
rs62621210	1.00[EUR][1000 genomes]
rs6459167	0.94[EUR][1000 genomes]
rs6459168	0.94[EUR][1000 genomes]
rs6900572	0.94[EUR][1000 genomes]
rs6903517	0.81[EUR][1000 genomes]
rs6903815	0.94[EUR][1000 genomes]
rs6941626	0.94[EUR][1000 genomes]
rs73455767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73455782	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73465854	1.00[EUR][1000 genomes]
rs73746926	0.94[EUR][1000 genomes]
rs73746929	0.94[EUR][1000 genomes]
rs73747826	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73747832	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749935	1.00[EUR][1000 genomes]
rs73749942	1.00[EUR][1000 genomes]
rs73749948	1.00[EUR][1000 genomes]
rs73749949	1.00[EUR][1000 genomes]
rs7749100	0.94[EUR][1000 genomes]
rs7759479	0.94[EUR][1000 genomes]
rs7760503	0.94[EUR][1000 genomes]
rs7760515	0.94[EUR][1000 genomes]
rs7760542	0.94[EUR][1000 genomes]
rs7760701	0.94[EUR][1000 genomes]
rs7761027	0.94[EUR][1000 genomes]
rs7769014	1.00[EUR][1000 genomes]
rs7775134	0.94[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	nsv830666	chr6:56243743-56419599	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv885912	chr6:56327849-56458836	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1016868	chr6:56376165-56417631	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56345000-56384200	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:56351800-56386800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:56357000-56382600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:56357000-56383600	Strong transcription	NH-A	brain
6	chr6:56357000-56384000	Strong transcription	HSMM	muscle
7	chr6:56357200-56384200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr6:56360400-56382200	Strong transcription	Osteobl	bone
9	chr6:56360600-56381800	Strong transcription	Muscle Satellite Cultured Cells	--
10	chr6:56360800-56377200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:56362400-56391200	Weak transcription	Esophagus	oesophagus
12	chr6:56362600-56385800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:56362800-56400200	Weak transcription	Colonic Mucosa	Colon
14	chr6:56363000-56402200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:56364800-56378600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:56365600-56379400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr6:56368400-56382400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:56369400-56378800	Strong transcription	Fetal Muscle Trunk	muscle
19	chr6:56369400-56380600	Strong transcription	HSMMtube	muscle
20	chr6:56370000-56378000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:56370000-56382600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr6:56370600-56380400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:56371000-56378000	Enhancers	Fetal Heart	heart
24	chr6:56371200-56380200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:56372200-56378000	Genic enhancers	Liver	Liver
26	chr6:56372200-56384200	Weak transcription	Hela-S3	cervix
27	chr6:56372800-56378600	Strong transcription	Adipose Nuclei	Adipose
28	chr6:56372800-56378800	Strong transcription	Fetal Muscle Leg	muscle
29	chr6:56372800-56380200	Weak transcription	Aorta	Aorta
30	chr6:56373000-56378200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:56373000-56378600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr6:56373000-56382800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr6:56373000-56390800	Weak transcription	Placenta	Placenta
34	chr6:56373600-56378600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:56373600-56379400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:56373800-56380200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:56374200-56383400	Weak transcription	Right Ventricle	heart
38	chr6:56374200-56387000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr6:56374200-56390800	Weak transcription	Lung	lung
40	chr6:56374200-56391000	Weak transcription	Right Atrium	heart
41	chr6:56374400-56378400	Weak transcription	NHEK	skin
42	chr6:56374400-56379200	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr6:56374400-56386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr6:56374400-56392000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:56374400-56396800	Weak transcription	Fetal Brain Female	brain
46	chr6:56374600-56377600	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:56374600-56377600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:56374600-56378600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:56374600-56379400	Weak transcription	Brain Germinal Matrix	brain
50	chr6:56374600-56379400	Weak transcription	Brain Inferior Temporal Lobe	brain

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