Variant report

Variant	rs3800026
Chromosome Location	chr6:56394669-56394670
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56386188..56388419-chr6:56391719..56395434,3	MCF-7	breast:
2	chr6:56379723..56396922-chr6:56400495..56411638,31	K562	blood:
3	chr1:222517973..222518488-chr6:56394311..56395250,2	MCF-7	breast:
4	chr6:56393226..56394746-chr6:56401973..56403869,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1024196	0.94[EUR][1000 genomes]
rs11963288	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11966986	0.94[EUR][1000 genomes]
rs11967796	0.94[EUR][1000 genomes]
rs11970410	0.94[EUR][1000 genomes]
rs12662511	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1407831	0.94[EUR][1000 genomes]
rs1535609	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs1535611	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16887928	0.94[EUR][1000 genomes]
rs16887983	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs16888070	0.94[EUR][1000 genomes]
rs16888106	0.94[EUR][1000 genomes]
rs17757606	0.95[ASN][1000 genomes]
rs17757660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17830661	0.95[ASN][1000 genomes]
rs17830685	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17830715	0.98[ASN][1000 genomes]
rs17830726	0.98[ASN][1000 genomes]
rs17830810	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][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]
rs3924307	1.00[EUR][1000 genomes]
rs41267673	0.94[EUR][1000 genomes]
rs41271848	0.94[EUR][1000 genomes]
rs41271850	0.94[EUR][1000 genomes]
rs41271854	1.00[EUR][1000 genomes]
rs41271856	1.00[EUR][1000 genomes]
rs41271872	0.94[EUR][1000 genomes]
rs41271876	0.94[EUR][1000 genomes]
rs41271878	0.94[EUR][1000 genomes]
rs4256439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4288197	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45442999	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[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[EUR][1000 genomes]
rs73455782	1.00[EUR][1000 genomes]
rs73465854	1.00[EUR][1000 genomes]
rs73746926	0.94[EUR][1000 genomes]
rs73746929	0.94[EUR][1000 genomes]
rs73747826	0.94[EUR][1000 genomes]
rs73747832	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	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7775134	0.94[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	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
5	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

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56341800-56407400	Weak transcription	Spleen	Spleen
2	chr6:56362800-56400200	Weak transcription	Colonic Mucosa	Colon
3	chr6:56363000-56402200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:56374400-56396800	Weak transcription	Fetal Brain Female	brain
5	chr6:56374600-56395200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:56374600-56399600	Weak transcription	Fetal Thymus	thymus
7	chr6:56376400-56407200	Weak transcription	Gastric	stomach
8	chr6:56377200-56404200	Weak transcription	K562	blood
9	chr6:56380600-56401200	Weak transcription	Psoas Muscle	Psoas
10	chr6:56383200-56396400	Weak transcription	Brain Germinal Matrix	brain
11	chr6:56383200-56402400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:56384400-56402200	Weak transcription	Small Intestine	intestine
13	chr6:56387200-56396800	Weak transcription	Hela-S3	cervix
14	chr6:56388000-56402200	Strong transcription	Fetal Intestine Large	intestine
15	chr6:56388200-56396400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:56388200-56401800	Strong transcription	Liver	Liver
17	chr6:56388800-56399600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:56390200-56397800	Strong transcription	Rectal Mucosa Donor 31	rectum
19	chr6:56390200-56401400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:56390200-56401600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:56390400-56398000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:56390400-56400000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr6:56390600-56394800	Genic enhancers	Colon Smooth Muscle	Colon
24	chr6:56390600-56395400	Strong transcription	HepG2	liver
25	chr6:56390600-56396400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr6:56390600-56403800	Weak transcription	Thymus	Thymus
27	chr6:56390800-56395400	Strong transcription	Placenta	Placenta
28	chr6:56390800-56395800	Genic enhancers	Osteobl	bone
29	chr6:56390800-56398400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr6:56390800-56402400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:56390800-56403000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:56391000-56395400	Genic enhancers	Muscle Satellite Cultured Cells	--
33	chr6:56391000-56397800	Weak transcription	Stomach Mucosa	stomach
34	chr6:56391000-56398000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr6:56391000-56398800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr6:56391200-56398600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:56391400-56394800	Strong transcription	HSMMtube	muscle
38	chr6:56391400-56395000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr6:56391400-56395200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr6:56391400-56396400	Weak transcription	Brain Angular Gyrus	brain
41	chr6:56391400-56396400	Weak transcription	A549	lung
42	chr6:56391400-56396600	Weak transcription	Aorta	Aorta
43	chr6:56391400-56396600	Weak transcription	Brain Hippocampus Middle	brain
44	chr6:56391400-56397800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr6:56391400-56398400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:56391400-56398600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:56391400-56400000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr6:56391400-56400800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr6:56391400-56400800	Weak transcription	Esophagus	oesophagus
50	chr6:56391400-56400800	Weak transcription	Right Ventricle	heart

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