Variant report

Variant	rs2252459
Chromosome Location	chr3:105246772-105246773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr3:105246753-105247263	HCT-116	colon:	n/a	chr3:105247230-105247244
2	PBX3	chr3:105246628-105247166	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr3:105246672-105247417	ECC-1	luminal epithelium:	n/a	chr3:105247083-105247100 chr3:105247084-105247100
4	MYC	chr3:105246698-105247211	MCF10A-Er-Src	breast:	n/a	chr3:105246763-105246773
5	KAP1	chr3:105246618-105247270	U2OS	brain:	n/a	n/a
6	NFIC	chr3:105246727-105247341	SK-N-SH	brain:	n/a	chr3:105247083-105247100 chr3:105247084-105247100

Variant related genes	Relation type
ALCAM	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1017913	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1017914	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1994317	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6793123	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9864062	0.85[JPT][hapmap]
rs9870921	0.85[JPT][hapmap];0.81[MEX][hapmap]

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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
3	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
7	chr3:105233400-105250600	Weak transcription	HSMM	muscle
8	chr3:105234200-105260400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:105234600-105260600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:105234600-105261000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:105234600-105274600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:105236200-105251000	Weak transcription	Aorta	Aorta
13	chr3:105236400-105251000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:105237800-105251000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:105237800-105259000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:105237800-105274600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:105237800-105275800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:105239400-105248000	Weak transcription	HUVEC	blood vessel
19	chr3:105240000-105252400	Weak transcription	Gastric	stomach
20	chr3:105241000-105260400	Weak transcription	Pancreas	Pancrea
21	chr3:105241200-105250600	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr3:105241600-105250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:105241600-105260200	Weak transcription	HepG2	liver
24	chr3:105241800-105259000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:105242000-105259800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:105242000-105293600	Weak transcription	Lung	lung
27	chr3:105242200-105252800	Weak transcription	Fetal Intestine Large	intestine
28	chr3:105242200-105259000	Weak transcription	Ovary	ovary
29	chr3:105242400-105256400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:105242400-105280400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:105242800-105266800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:105243200-105248400	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:105243200-105259000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr3:105244200-105248800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:105244600-105252000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:105244800-105247600	Enhancers	Osteobl	bone
37	chr3:105244800-105275800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:105245000-105258800	Weak transcription	Primary B cells from cord blood	blood
39	chr3:105245200-105248000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:105245200-105250800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:105245200-105259200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:105245400-105247200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:105245400-105248000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:105245400-105248000	Enhancers	Hela-S3	cervix
45	chr3:105245400-105248000	Enhancers	HMEC	breast
46	chr3:105245400-105250800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:105245400-105251000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:105245400-105252600	Weak transcription	Fetal Brain Male	brain
49	chr3:105245600-105246800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:105245600-105247200	Enhancers	NH-A	brain

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