Variant report

Variant	rs60425255
Chromosome Location	chr3:28285102-28285103
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:28239745..28241981-chr3:28283804..28285570,2	K562	blood:
2	chr3:28281324..28283221-chr3:28283797..28285477,2	MCF-7	breast:
3	chr3:27809091..27811798-chr3:28283173..28285576,2	MCF-7	breast:
4	chr3:28283572..28286334-chr3:28300676..28304694,4	K562	blood:
5	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:
6	chr3:28284090..28285869-chr3:28364556..28366935,2	K562	blood:

Variant related genes	Relation type
ENSG00000206559	Chromatin interaction
ENSG00000163512	Chromatin interaction
ENSG00000187118	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10510606	0.86[AFR][1000 genomes]
rs11129312	0.86[AFR][1000 genomes]
rs11129314	0.84[AFR][1000 genomes]
rs11708368	0.86[AFR][1000 genomes]
rs11717202	0.86[AFR][1000 genomes]
rs11921526	0.87[AFR][1000 genomes]
rs12485853	0.86[AFR][1000 genomes]
rs12497510	0.87[AFR][1000 genomes]
rs12498078	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13069777	0.87[AFR][1000 genomes]
rs13085236	0.82[AFR][1000 genomes]
rs13092179	0.87[AFR][1000 genomes]
rs1606391	0.86[AFR][1000 genomes]
rs2220742	0.83[ASN][1000 genomes]
rs4680748	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6782956	0.86[AFR][1000 genomes]
rs6785465	0.87[AFR][1000 genomes]
rs6792110	0.86[AFR][1000 genomes]
rs6798266	0.86[AFR][1000 genomes]
rs6800659	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810242	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7633786	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9637515	0.83[ASN][1000 genomes]
rs966029	0.84[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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28283800-28311400	Weak transcription	Lung	lung
2	chr3:28284000-28285200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:28284000-28285200	Enhancers	Primary hematopoietic stem cells	blood
4	chr3:28284000-28285200	Enhancers	Fetal Thymus	thymus
5	chr3:28284000-28285600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr3:28284000-28285800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:28284000-28285800	Enhancers	Thymus	Thymus
8	chr3:28284000-28286000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:28284000-28286000	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:28284000-28286000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:28284000-28286000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr3:28284000-28286200	Enhancers	Pancreas	Pancrea
13	chr3:28284000-28286400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:28284000-28286400	Weak transcription	HSMM	muscle
15	chr3:28284000-28286600	Weak transcription	Brain Angular Gyrus	brain
16	chr3:28284000-28287000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:28284000-28290000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr3:28284000-28290800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr3:28284000-28304800	Weak transcription	Primary B cells from cord blood	blood
20	chr3:28284000-28309600	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:28284000-28313800	Weak transcription	Ovary	ovary
22	chr3:28284000-28317200	Weak transcription	Gastric	stomach
23	chr3:28284200-28285400	Transcr. at gene 5' and 3'	K562	blood
24	chr3:28284200-28285800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:28284200-28286000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr3:28284200-28286200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:28284200-28286200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:28284200-28286800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:28284200-28287200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr3:28284200-28287400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr3:28284200-28288600	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:28284200-28288800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:28284200-28292600	Weak transcription	Psoas Muscle	Psoas
34	chr3:28284200-28292800	Weak transcription	Small Intestine	intestine
35	chr3:28284400-28285200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:28284400-28285200	Enhancers	Primary T cells from cord blood	blood
37	chr3:28284400-28285200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:28284400-28285400	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr3:28284400-28285400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:28284400-28285400	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:28284400-28285600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:28284400-28285600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:28284400-28285600	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr3:28284400-28285600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:28284400-28285600	Active TSS	GM12878-XiMat	blood
46	chr3:28284400-28285800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:28284400-28286200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr3:28284400-28286400	Enhancers	Primary T cells fromperipheralblood	blood
49	chr3:28284400-28286400	Enhancers	Fetal Heart	heart
50	chr3:28284400-28286600	Weak transcription	Stomach Mucosa	stomach

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