Variant report

Variant	rs12475787
Chromosome Location	chr2:55247257-55247258
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55246557..55249520-chr2:55255135..55258063,3	MCF-7	breast:
2	chr2:55240610..55242717-chr2:55245161..55247325,2	K562	blood:
3	chr2:55243678..55249957-chr2:55274888..55279397,9	MCF-7	breast:
4	chr2:55244120..55248820-chr2:55275882..55279343,5	K562	blood:
5	chr2:55245145..55247960-chr2:55267490..55269822,3	K562	blood:
6	chr2:55242881..55244932-chr2:55247245..55249562,2	K562	blood:
7	chr2:55245750..55247978-chr2:55249196..55251041,2	MCF-7	breast:
8	chr2:55234040..55237734-chr2:55246769..55250149,4	K562	blood:
9	chr2:55245814..55247960-chr2:55267490..55269701,2	K562	blood:
10	chr2:55245733..55248128-chr2:55275141..55278427,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000200086	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10189379	0.85[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs10496036	0.96[CEU][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs12464447	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12464595	0.92[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs12475904	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12479297	0.94[ASN][1000 genomes]
rs17046570	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17046594	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17347089	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17418675	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2289747	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55659423	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55698303	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55993793	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56013263	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6545467	0.81[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs6707036	0.85[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs67156582	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6730728	0.94[ASN][1000 genomes]
rs72795431	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72795440	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7582359	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs7584354	0.92[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7584386	0.92[CHB][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7601625	0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs887	0.93[GIH][hapmap];0.89[TSI][hapmap];0.83[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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
3	chr2:55237600-55249600	Weak transcription	Gastric	stomach
4	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:55237600-55258600	Weak transcription	Ovary	ovary
6	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
7	chr2:55238400-55249200	Weak transcription	Pancreas	Pancrea
8	chr2:55238400-55249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:55238400-55250800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:55238400-55251200	Weak transcription	Psoas Muscle	Psoas
11	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
12	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
13	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:55239200-55247800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:55240400-55249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:55240400-55249800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:55240600-55249000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:55240800-55249600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:55240800-55250200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:55241000-55249000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:55241000-55249000	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr2:55241000-55249600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
24	chr2:55241200-55247400	Weak transcription	Fetal Intestine Large	intestine
25	chr2:55241200-55247800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:55241200-55249000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr2:55241200-55249200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:55241200-55249600	Weak transcription	Fetal Heart	heart
29	chr2:55241400-55249200	Weak transcription	Primary T cells from cord blood	blood
30	chr2:55241400-55253400	Weak transcription	Fetal Lung	lung
31	chr2:55241800-55247800	Weak transcription	Lung	lung
32	chr2:55242000-55252400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr2:55242200-55249800	Weak transcription	Fetal Brain Male	brain
34	chr2:55242200-55253400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:55242400-55253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:55242600-55248600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:55242800-55249000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:55243000-55249200	Weak transcription	Small Intestine	intestine
40	chr2:55243000-55250000	Weak transcription	Colon Smooth Muscle	Colon
41	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
42	chr2:55243200-55252600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr2:55243600-55249400	Weak transcription	Spleen	Spleen
44	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:55244200-55247400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:55244400-55247800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:55244600-55248800	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:55244600-55249000	Strong transcription	Fetal Brain Female	brain
49	chr2:55244800-55248200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr2:55244800-55249600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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