Variant report

Variant	rs41271850
Chromosome Location	chr6:56329654-56329655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1024196	0.89[EUR][1000 genomes]
rs11963288	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11966986	0.89[EUR][1000 genomes]
rs11967796	0.89[EUR][1000 genomes]
rs11970410	0.89[EUR][1000 genomes]
rs1407831	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1535609	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1535611	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16887928	1.00[EUR][1000 genomes]
rs16888070	0.89[EUR][1000 genomes]
rs16888106	0.89[EUR][1000 genomes]
rs2144407	0.89[EUR][1000 genomes]
rs2180148	0.89[EUR][1000 genomes]
rs2207678	0.89[EUR][1000 genomes]
rs2397224	1.00[EUR][1000 genomes]
rs28633631	0.89[EUR][1000 genomes]
rs3800026	0.94[EUR][1000 genomes]
rs3924307	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41267673	0.89[EUR][1000 genomes]
rs41271848	1.00[EUR][1000 genomes]
rs41271854	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41271856	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41271872	0.89[EUR][1000 genomes]
rs41271876	0.89[EUR][1000 genomes]
rs41271878	0.89[EUR][1000 genomes]
rs4256439	0.94[EUR][1000 genomes]
rs4288197	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs45442999	0.94[EUR][1000 genomes]
rs45553042	0.84[EUR][1000 genomes]
rs57289287	0.89[EUR][1000 genomes]
rs57350484	0.89[EUR][1000 genomes]
rs57790896	0.89[EUR][1000 genomes]
rs57822928	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58565063	0.89[EUR][1000 genomes]
rs58730144	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59772940	0.89[EUR][1000 genomes]
rs59864125	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62621210	0.94[EUR][1000 genomes]
rs6459167	0.89[EUR][1000 genomes]
rs6459168	0.89[EUR][1000 genomes]
rs6900572	0.89[EUR][1000 genomes]
rs6903815	0.89[EUR][1000 genomes]
rs6941626	0.89[EUR][1000 genomes]
rs73455767	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73455782	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73465854	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73746926	0.89[EUR][1000 genomes]
rs73746929	0.89[EUR][1000 genomes]
rs73747826	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73747832	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73749926	0.84[AFR][1000 genomes]
rs73749935	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749942	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749948	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73749949	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7749100	0.89[EUR][1000 genomes]
rs7759479	0.89[EUR][1000 genomes]
rs7760503	0.89[EUR][1000 genomes]
rs7760515	0.89[EUR][1000 genomes]
rs7760542	0.89[EUR][1000 genomes]
rs7760701	0.89[EUR][1000 genomes]
rs7761027	0.89[EUR][1000 genomes]
rs7769014	0.94[EUR][1000 genomes]
rs7775134	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56308800-56373800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:56315000-56347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:56315000-56349800	Strong transcription	HSMM	muscle
4	chr6:56315600-56371000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:56316800-56337600	Weak transcription	Hela-S3	cervix
6	chr6:56317200-56342800	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr6:56317800-56331200	Strong transcription	HSMMtube	muscle
8	chr6:56318000-56340600	Strong transcription	Fetal Intestine Large	intestine
9	chr6:56318600-56331000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:56318800-56332000	Strong transcription	Fetal Lung	lung
11	chr6:56319000-56331200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:56319000-56348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:56319200-56331200	Strong transcription	Osteobl	bone
14	chr6:56319200-56340400	Strong transcription	NH-A	brain
15	chr6:56319200-56348400	Strong transcription	NHDF-Ad	bronchial
16	chr6:56319400-56343600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:56319400-56344200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:56320000-56338800	Strong transcription	Liver	Liver
19	chr6:56320800-56331200	Strong transcription	Brain Anterior Caudate	brain
20	chr6:56321000-56331000	Strong transcription	Stomach Smooth Muscle	stomach
21	chr6:56321000-56331200	Strong transcription	Fetal Muscle Leg	muscle
22	chr6:56321000-56331200	Strong transcription	Left Ventricle	heart
23	chr6:56321000-56331800	Strong transcription	Brain Hippocampus Middle	brain
24	chr6:56321000-56343400	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr6:56321200-56343800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:56321800-56331800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:56322000-56330000	Strong transcription	Brain Cingulate Gyrus	brain
28	chr6:56322000-56330800	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr6:56322000-56331600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr6:56322000-56332400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr6:56322200-56331400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr6:56322200-56332200	Strong transcription	GM12878-XiMat	blood
33	chr6:56322200-56339000	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:56322200-56349200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:56322400-56344200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:56322600-56348200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:56322800-56331000	Strong transcription	HepG2	liver
38	chr6:56323000-56331800	Strong transcription	HMEC	breast
39	chr6:56323600-56331200	Strong transcription	Colon Smooth Muscle	Colon
40	chr6:56324000-56333600	Weak transcription	Psoas Muscle	Psoas
41	chr6:56324200-56331200	Strong transcription	Brain Angular Gyrus	brain
42	chr6:56324600-56331600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:56324800-56336800	Weak transcription	Gastric	stomach
44	chr6:56324800-56340400	Weak transcription	Spleen	Spleen
45	chr6:56325000-56340000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:56325000-56346600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:56325200-56333400	Weak transcription	Fetal Heart	heart
48	chr6:56325200-56336200	Weak transcription	Fetal Brain Female	brain
49	chr6:56326600-56330200	Strong transcription	HUVEC	blood vessel
50	chr6:56326600-56330400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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