Variant report

Variant	rs1343799
Chromosome Location	chr6:45421630-45421631
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45412131..45416669-chr6:45417302..45422043,11	K562	blood:
2	chr6:45344104..45346279-chr6:45419822..45423206,3	K562	blood:
3	chr6:45410613..45412581-chr6:45419740..45423664,4	MCF-7	breast:
4	chr6:45415640..45418079-chr6:45419010..45422483,4	MCF-7	breast:
5	chr6:45404679..45406286-chr6:45420407..45423168,2	K562	blood:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10214519	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12197948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12210100	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12215249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1317777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13208741	1.00[JPT][hapmap]
rs1934327	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2252718	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2256819	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2396442	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2677098	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677099	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677100	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2677109	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2677110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790094	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2790095	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2790097	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2790098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790099	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2790100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790102	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2790103	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2819852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819865	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2819866	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2819867	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820339	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2820340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711816	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4714854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6458443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765724	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756144	0.90[EUR][1000 genomes]
rs910586	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9472494	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9885645	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45399400-45423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:45407200-45462000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:45413400-45423400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:45414000-45431400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:45415000-45421800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:45415200-45421800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:45415200-45421800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:45415200-45422200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:45415200-45422200	Weak transcription	HMEC	breast
10	chr6:45415600-45424600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:45415800-45421800	Weak transcription	NHEK	skin
12	chr6:45416000-45421800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:45416200-45421800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:45416400-45421800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:45416400-45430600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:45416400-45440400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:45416600-45430000	Weak transcription	Small Intestine	intestine
18	chr6:45417200-45422400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:45417400-45421800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:45417600-45422200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:45418200-45427400	Weak transcription	Aorta	Aorta
22	chr6:45419000-45422800	Genic enhancers	HSMM	muscle
23	chr6:45419200-45456200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr6:45419400-45429000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:45419800-45422200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:45419800-45423600	Enhancers	Hela-S3	cervix
27	chr6:45420000-45421800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:45420000-45422400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:45420000-45425200	Strong transcription	Dnd41	blood
30	chr6:45420200-45422600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:45420200-45423000	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:45420400-45423000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr6:45420600-45421800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr6:45420600-45422000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr6:45420600-45422200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:45420600-45422600	Enhancers	NHDF-Ad	bronchial
37	chr6:45420600-45423400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr6:45420600-45423400	Enhancers	K562	blood
39	chr6:45420800-45422600	Enhancers	HSMMtube	muscle
40	chr6:45420800-45423000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:45420800-45424200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:45420800-45425600	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr6:45421000-45422000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:45421000-45422600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:45421000-45422600	Enhancers	NHLF	lung
46	chr6:45421200-45421800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:45421200-45421800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:45421200-45422000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:45421200-45422000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr6:45421200-45422600	Enhancers	HUVEC	blood vessel

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