Variant report

Variant	rs6709533
Chromosome Location	chr2:58435543-58435544
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58390705..58393005-chr2:58433793..58436781,2	K562	blood:

Variant related genes	Relation type
ENSG00000115392	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10184957	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11903212	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12616896	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12624152	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713376	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12988249	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13006005	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13023405	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032851	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13397947	0.80[AFR][1000 genomes]
rs13410228	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13422760	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1404457	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1404459	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1404460	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34335951	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34556232	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35341336	0.82[EUR][1000 genomes]
rs35773188	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35925771	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755296	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771222	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55809167	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57267169	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61746304	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6714952	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6740373	0.84[AFR][1000 genomes]
rs6740836	0.84[AFR][1000 genomes]
rs6742445	0.93[AFR][1000 genomes]
rs6752935	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72948876	0.91[AFR][1000 genomes]
rs7340170	0.90[AFR][1000 genomes]
rs7558066	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7561771	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7590976	0.91[AFR][1000 genomes]
rs7597069	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr2:58391000-58467000	Weak transcription	HMEC	breast
5	chr2:58396400-58438000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:58396400-58438000	Weak transcription	Pancreas	Pancrea
7	chr2:58397800-58442600	Weak transcription	Brain Anterior Caudate	brain
8	chr2:58398000-58437800	Weak transcription	Primary B cells from cord blood	blood
9	chr2:58399400-58437400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:58400400-58437800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:58403000-58439400	Weak transcription	HSMM	muscle
12	chr2:58403600-58437200	Weak transcription	Fetal Brain Female	brain
13	chr2:58411600-58437400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:58413800-58438000	Weak transcription	Thymus	Thymus
15	chr2:58414000-58437600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:58414000-58461400	Weak transcription	NHEK	skin
17	chr2:58414200-58435800	Weak transcription	Fetal Intestine Small	intestine
18	chr2:58414400-58438000	Weak transcription	Esophagus	oesophagus
19	chr2:58414600-58437400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr2:58414600-58437400	Weak transcription	Brain Germinal Matrix	brain
21	chr2:58415000-58437600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:58415800-58437400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:58416000-58437400	Weak transcription	Fetal Kidney	kidney
24	chr2:58416200-58437400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:58416200-58454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:58416400-58437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:58416400-58438000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr2:58416600-58467200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:58417800-58439200	Weak transcription	Fetal Brain Male	brain
30	chr2:58421600-58452400	Weak transcription	NH-A	brain
31	chr2:58422000-58437400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr2:58422000-58442800	Weak transcription	Brain Angular Gyrus	brain
33	chr2:58422000-58454200	Weak transcription	Left Ventricle	heart
34	chr2:58423800-58437400	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:58425000-58442200	Weak transcription	Fetal Heart	heart
36	chr2:58425400-58438400	Weak transcription	Ovary	ovary
37	chr2:58425600-58446600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:58425800-58446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:58426000-58437200	Weak transcription	GM12878-XiMat	blood
40	chr2:58426000-58437400	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:58426400-58437400	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:58426400-58438000	Weak transcription	Fetal Intestine Large	intestine
43	chr2:58426600-58436000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:58429200-58438000	Weak transcription	Fetal Stomach	stomach
45	chr2:58429600-58439600	Weak transcription	Adipose Nuclei	Adipose
46	chr2:58430000-58436200	Weak transcription	Brain Substantia Nigra	brain
47	chr2:58430000-58440400	Weak transcription	Hela-S3	cervix
48	chr2:58430200-58436800	Weak transcription	Liver	Liver
49	chr2:58430600-58438000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:58431200-58437200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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