Variant report

Variant	rs28370012
Chromosome Location	chr1:223902973-223902974
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223901494..223903169-chr1:223928356..223930429,2	MCF-7	breast:
2	chr1:223884407..223886063-chr1:223901694..223904527,2	K562	blood:
3	chr1:223902474..223903675-chr1:223936616..223937446,3	MCF-7	breast:
4	chr1:223902286..223903884-chr1:223996819..223998348,2	K562	blood:
5	chr1:223900571..223903093-chr1:223940555..223942413,2	K562	blood:
6	chr1:223887434..223890501-chr1:223901110..223904266,3	K562	blood:
7	chr1:223901364..223903173-chr1:224031869..224034439,2	K562	blood:
8	chr1:223900402..223903093-chr1:223939885..223943104,3	K562	blood:
9	chr1:223900439..223903816-chr1:223918326..223920507,3	MCF-7	breast:
10	chr1:223901725..223903941-chr1:223941728..223943865,2	MCF-7	breast:
11	chr1:223901424..223903659-chr1:224301052..224303387,3	K562	blood:
12	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
13	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:
14	chr1:223901394..223904242-chr1:223919607..223921227,2	K562	blood:
15	chr1:223901244..223903074-chr1:224621960..224624897,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction
ENSG00000143786	Chromatin interaction
ENSG00000143756	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10916601	0.96[ASN][1000 genomes]
rs10916602	0.96[ASN][1000 genomes]
rs10916604	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11579787	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11580689	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11581716	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11589956	0.85[EUR][1000 genomes]
rs12057708	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12074091	0.96[ASN][1000 genomes]
rs12080565	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs16842040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16842062	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1892077	0.96[ASN][1000 genomes]
rs2000320	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2154113	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2154114	0.81[ASN][1000 genomes]
rs2186006	0.96[ASN][1000 genomes]
rs2275877	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370013	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370014	0.96[ASN][1000 genomes]
rs28370020	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28370029	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4653499	0.96[ASN][1000 genomes]
rs61823966	0.96[ASN][1000 genomes]
rs6669046	0.82[ASN][1000 genomes]
rs6674733	0.82[ASN][1000 genomes]
rs7366009	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7414311	0.96[ASN][1000 genomes]
rs7555491	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223900800-223903000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr1:223900800-223903400	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr1:223900800-223903400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr1:223900800-223904400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:223900800-223906000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:223901000-223903400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:223901000-223903800	Flanking Active TSS	HUVEC	blood vessel
8	chr1:223901000-223904200	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr1:223901000-223905200	Enhancers	Spleen	Spleen
10	chr1:223901000-223905800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr1:223901200-223903400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr1:223901200-223904600	Enhancers	Small Intestine	intestine
13	chr1:223901200-223904800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:223901200-223905400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:223901400-223904400	Transcr. at gene 5' and 3'	NHLF	lung
16	chr1:223901400-223904800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
17	chr1:223901400-223905600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
19	chr1:223901600-223903000	Flanking Active TSS	HMEC	breast
20	chr1:223901600-223903400	Enhancers	Pancreas	Pancrea
21	chr1:223901600-223903600	Enhancers	Ovary	ovary
22	chr1:223901600-223903600	Flanking Active TSS	NH-A	brain
23	chr1:223901600-223903800	Enhancers	Primary T cells from cord blood	blood
24	chr1:223901600-223903800	Enhancers	Fetal Intestine Small	intestine
25	chr1:223901600-223904000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:223901600-223904200	Enhancers	Brain Angular Gyrus	brain
27	chr1:223901600-223904200	Enhancers	Placenta	Placenta
28	chr1:223901600-223904600	Enhancers	Brain Hippocampus Middle	brain
29	chr1:223901600-223905200	Transcr. at gene 5' and 3'	NHEK	skin
30	chr1:223901600-223905800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:223901600-223906200	Enhancers	Primary B cells from peripheral blood	blood
32	chr1:223901600-223906400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr1:223901800-223903000	Weak transcription	Brain Germinal Matrix	brain
34	chr1:223901800-223903200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:223901800-223903200	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr1:223901800-223903400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:223901800-223903600	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:223901800-223903600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:223901800-223903600	Transcr. at gene 5' and 3'	K562	blood
40	chr1:223901800-223903800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr1:223901800-223904000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:223901800-223904000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:223901800-223904000	Weak transcription	Aorta	Aorta
44	chr1:223901800-223904000	Enhancers	Brain Cingulate Gyrus	brain
45	chr1:223901800-223904000	Enhancers	Fetal Intestine Large	intestine
46	chr1:223901800-223904000	Transcr. at gene 5' and 3'	Osteobl	bone
47	chr1:223901800-223904200	Enhancers	Lung	lung
48	chr1:223901800-223904400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:223901800-223904600	Enhancers	Right Atrium	heart
50	chr1:223901800-223904800	Enhancers	Fetal Brain Female	brain

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