Variant report

Variant	rs6005900
Chromosome Location	chr22:29215249-29215250
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29215019..29217111-chr22:29277896..29279810,2	MCF-7	breast:
2	chr22:28995342..28997582-chr22:29214405..29215908,2	MCF-7	breast:
3	chr22:29196125..29197020-chr22:29214940..29215805,2	MCF-7	breast:
4	chr22:29167538..29169220-chr22:29214711..29217265,3	MCF-7	breast:
5	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
6	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
7	chr17:56735334..56737625-chr22:29214146..29217564,3	MCF-7	breast:
8	chr22:29214264..29215838-chr9:132244922..132247103,2	MCF-7	breast:
9	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000100209	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000204054	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12159764	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16986714	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1894590	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2269575	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41281601	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4484131	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57652775	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59954406	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997399	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997400	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5997403	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5997404	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005875	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005876	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6005878	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005879	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005893	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005905	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005906	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005907	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005915	0.82[AFR][1000 genomes]
rs6005918	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6005920	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60513698	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6519764	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7284322	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7290019	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7290679	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7290958	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7291783	0.82[ASN][1000 genomes]
rs73388819	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73388827	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388828	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388838	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388841	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73388872	0.80[EUR][1000 genomes]
rs73399615	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73399621	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9941965	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29198000-29225200	Weak transcription	HSMM	muscle
4	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
5	chr22:29198400-29215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr22:29198600-29219400	Weak transcription	NHLF	lung
8	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr22:29198600-29225200	Weak transcription	Osteobl	bone
10	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
11	chr22:29198800-29230800	Weak transcription	NHEK	skin
12	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:29205200-29218800	Weak transcription	Brain Hippocampus Middle	brain
14	chr22:29205400-29217000	Weak transcription	Gastric	stomach
15	chr22:29205400-29225600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr22:29206200-29215600	Enhancers	Stomach Mucosa	stomach
17	chr22:29208200-29221000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr22:29208400-29217000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr22:29211400-29215600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr22:29211400-29216200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr22:29211600-29218800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr22:29211800-29219200	Enhancers	Fetal Thymus	thymus
23	chr22:29211800-29225600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:29212000-29225200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr22:29212600-29215800	Enhancers	Thymus	Thymus
26	chr22:29212600-29216400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr22:29212600-29216400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr22:29212800-29215800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr22:29212800-29216000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr22:29213000-29215800	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr22:29213600-29216000	Enhancers	Placenta	Placenta
32	chr22:29213600-29216000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr22:29213600-29216400	Enhancers	Fetal Intestine Large	intestine
34	chr22:29213600-29216400	Enhancers	Fetal Intestine Small	intestine
35	chr22:29213600-29220600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr22:29213800-29216000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr22:29213800-29216200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr22:29213800-29216200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr22:29214000-29215400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr22:29214000-29215800	Enhancers	Primary hematopoietic stem cells	blood
41	chr22:29214000-29216000	Enhancers	Primary B cells from peripheral blood	blood
42	chr22:29214000-29216000	Enhancers	Primary T cells from cord blood	blood
43	chr22:29214000-29216000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr22:29214000-29216200	Enhancers	Duodenum Mucosa	Duodenum
45	chr22:29214000-29216400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr22:29214000-29218600	Enhancers	Liver	Liver
47	chr22:29214000-29219200	Enhancers	Pancreas	Pancrea
48	chr22:29214200-29215400	Enhancers	A549	lung
49	chr22:29214200-29215600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr22:29214200-29215600	Enhancers	Fetal Muscle Leg	muscle

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