Variant report

Variant	rs2252088
Chromosome Location	chr12:104252962-104252963
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104221407..104223311-chr12:104252551..104254594,2	MCF-7	breast:
2	chr12:104252726..104255857-chr12:104256920..104259686,3	MCF-7	breast:
3	chr12:104252627..104253426-chr6:163440642..163441162,2	MCF-7	breast:
4	chr12:104252720..104255183-chr12:104502836..104504925,2	K562	blood:
5	chr12:104234105..104239098-chr12:104250004..104255076,13	MCF-7	breast:
6	chr12:104247921..104249635-chr12:104251344..104253746,2	MCF-7	breast:
7	chr12:104250532..104253421-chr12:104255015..104257063,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction
ENSG00000257327	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10745982	0.85[EUR][1000 genomes]
rs10745983	0.83[EUR][1000 genomes]
rs10778291	0.84[EUR][1000 genomes]
rs10778293	0.85[EUR][1000 genomes]
rs10778294	0.85[EUR][1000 genomes]
rs10778295	0.83[EUR][1000 genomes]
rs10861128	0.85[EUR][1000 genomes]
rs10861129	0.85[EUR][1000 genomes]
rs11111816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11111817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1165596	0.85[EUR][1000 genomes]
rs1165597	0.85[EUR][1000 genomes]
rs1165598	0.85[EUR][1000 genomes]
rs1185985	0.85[EUR][1000 genomes]
rs12312978	0.85[EUR][1000 genomes]
rs1583599	0.85[EUR][1000 genomes]
rs1595338	0.85[EUR][1000 genomes]
rs1595339	0.85[EUR][1000 genomes]
rs2196614	0.85[EUR][1000 genomes]
rs2248382	0.85[EUR][1000 genomes]
rs2251979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2263954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374353	0.85[EUR][1000 genomes]
rs2438116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2438389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439622	0.84[EUR][1000 genomes]
rs2576950	0.84[EUR][1000 genomes]
rs2576957	0.84[EUR][1000 genomes]
rs2576958	0.84[EUR][1000 genomes]
rs2576960	0.84[EUR][1000 genomes]
rs2576961	0.84[EUR][1000 genomes]
rs2576962	0.84[EUR][1000 genomes]
rs2576963	0.84[EUR][1000 genomes]
rs2576964	0.84[EUR][1000 genomes]
rs2576965	0.83[EUR][1000 genomes]
rs2576967	0.83[EUR][1000 genomes]
rs2583240	0.84[EUR][1000 genomes]
rs2583241	0.84[EUR][1000 genomes]
rs2583242	0.83[EUR][1000 genomes]
rs2583243	0.84[EUR][1000 genomes]
rs2583245	0.84[EUR][1000 genomes]
rs2583246	0.84[EUR][1000 genomes]
rs2583247	0.84[EUR][1000 genomes]
rs2583248	0.84[EUR][1000 genomes]
rs2583250	0.81[EUR][1000 genomes]
rs4316574	0.84[EUR][1000 genomes]
rs4488278	0.84[EUR][1000 genomes]
rs4556622	0.85[EUR][1000 genomes]
rs6539104	0.98[ASN][1000 genomes]
rs728165	0.85[EUR][1000 genomes]
rs7301119	0.94[ASN][1000 genomes]
rs7957036	0.95[ASN][1000 genomes]
rs7967501	0.85[EUR][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	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104236000-104253600	Weak transcription	Gastric	stomach
2	chr12:104240000-104254800	Enhancers	Rectal Smooth Muscle	rectum
3	chr12:104246600-104253200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:104246800-104254000	Weak transcription	Brain Anterior Caudate	brain
5	chr12:104250000-104257000	Weak transcription	Pancreas	Pancrea
6	chr12:104250000-104263800	Weak transcription	Liver	Liver
7	chr12:104250400-104254000	Weak transcription	Ovary	ovary
8	chr12:104251000-104253400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:104251200-104254400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:104251400-104254400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:104252000-104254000	Enhancers	HSMMtube	muscle
12	chr12:104252000-104254400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr12:104252200-104254400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:104252200-104254400	Enhancers	HSMM	muscle
15	chr12:104252200-104254600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:104252200-104254800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:104252200-104254800	Enhancers	Stomach Smooth Muscle	stomach
18	chr12:104252200-104255000	Enhancers	HMEC	breast
19	chr12:104252200-104255800	Enhancers	Placenta	Placenta
20	chr12:104252400-104253800	Enhancers	Fetal Intestine Large	intestine
21	chr12:104252400-104254000	Enhancers	Rectal Mucosa Donor 29	rectum
22	chr12:104252400-104254000	Enhancers	NH-A	brain
23	chr12:104252400-104254200	Enhancers	NHLF	lung
24	chr12:104252400-104254400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:104252400-104254400	Enhancers	NHDF-Ad	bronchial
26	chr12:104252400-104255000	Enhancers	Colon Smooth Muscle	Colon
27	chr12:104252600-104253000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr12:104252600-104253000	Flanking Active TSS	A549	lung
29	chr12:104252600-104253200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:104252600-104253200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr12:104252600-104253400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:104252600-104253600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:104252600-104253800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:104252600-104253800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:104252600-104253800	Enhancers	Fetal Intestine Small	intestine
36	chr12:104252600-104253800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:104252600-104253800	Enhancers	HUVEC	blood vessel
38	chr12:104252600-104253800	Enhancers	K562	blood
39	chr12:104252600-104254000	Enhancers	Osteobl	bone
40	chr12:104252600-104254400	Enhancers	Esophagus	oesophagus
41	chr12:104252600-104254400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr12:104252600-104254800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:104252600-104255000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:104252800-104253000	Flanking Active TSS	Hela-S3	cervix
45	chr12:104252800-104253000	Flanking Active TSS	HepG2	liver
46	chr12:104252800-104253000	Flanking Active TSS	NHEK	skin
47	chr12:104252800-104253600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr12:104252800-104253800	Enhancers	Stomach Mucosa	stomach
49	chr12:104252800-104254400	Enhancers	Fetal Stomach	stomach

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