Variant report

Variant	rs2269683
Chromosome Location	chr12:51417808-51417809
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51417420..51423779-chr12:51473917..51478493,9	MCF-7	breast:
2	chr12:51414500..51424231-chr12:51435741..51444321,19	K562	blood:
3	chr12:51404460..51409575-chr12:51416331..51420356,8	MCF-7	breast:
4	chr12:51416514..51419391-chr12:51663583..51665592,2	MCF-7	breast:
5	chr12:51417478..51420284-chr12:51632474..51634014,2	MCF-7	breast:
6	chr12:51158188..51159927-chr12:51415849..51417938,2	K562	blood:
7	chr12:51155914..51160622-chr12:51417270..51421869,9	K562	blood:
8	chr12:51416659..51422801-chr12:51440164..51444812,17	MCF-7	breast:
9	chr12:51398011..51404686-chr12:51416862..51423754,14	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272028	Chromatin interaction
ENSG00000123268	Chromatin interaction
ENSG00000050426	Chromatin interaction
ENSG00000110925	Chromatin interaction
ENSG00000170545	Chromatin interaction
ENSG00000183283	Chromatin interaction
ENSG00000110911	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10876122	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169625	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169629	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169634	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169640	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169643	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169651	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169662	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169681	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11169687	0.80[AMR][1000 genomes]
rs11169688	0.80[AMR][1000 genomes]
rs11169708	0.91[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap]
rs12227734	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1982777	0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2016533	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2239860	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269682	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2452795	0.81[TSI][hapmap]
rs2640525	0.81[TSI][hapmap]
rs2640526	0.81[TSI][hapmap]
rs3809320	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768871	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4768957	1.00[LWK][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap]
rs7295893	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7399214	0.81[TSI][hapmap]
rs8490	0.92[LWK][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap]

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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51399200-51418000	Weak transcription	Gastric	stomach
2	chr12:51402000-51418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:51402000-51418000	Weak transcription	Fetal Stomach	stomach
4	chr12:51402400-51418000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:51403000-51418000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:51407000-51418000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:51410800-51418400	Weak transcription	Primary B cells from cord blood	blood
8	chr12:51412600-51418400	Enhancers	Primary hematopoietic stem cells	blood
9	chr12:51412800-51418000	Enhancers	Primary T cells from cord blood	blood
10	chr12:51413200-51418400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr12:51413800-51418000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:51414400-51418000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr12:51415400-51418200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:51416000-51418000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:51416000-51418000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:51416000-51419400	Weak transcription	Spleen	Spleen
17	chr12:51416200-51418200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:51416200-51418400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:51416800-51418000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr12:51416800-51418000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:51416800-51418000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:51417000-51418000	Enhancers	Brain Germinal Matrix	brain
23	chr12:51417000-51418000	Enhancers	Placenta	Placenta
24	chr12:51417000-51418000	Enhancers	Pancreas	Pancrea
25	chr12:51417000-51418000	Enhancers	Psoas Muscle	Psoas
26	chr12:51417000-51418000	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr12:51417000-51418400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:51417000-51418400	Enhancers	Fetal Muscle Leg	muscle
29	chr12:51417200-51418000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr12:51417200-51418000	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr12:51417200-51418000	Enhancers	Stomach Mucosa	stomach
32	chr12:51417200-51418000	Genic enhancers	Dnd41	blood
33	chr12:51417200-51418400	Enhancers	Fetal Brain Male	brain
34	chr12:51417200-51418800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr12:51417200-51419800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr12:51417400-51418000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:51417400-51418000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:51417400-51418000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:51417400-51418000	Enhancers	Adipose Nuclei	Adipose
40	chr12:51417400-51418000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr12:51417400-51418000	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr12:51417400-51418200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:51417400-51418200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:51417400-51418200	Flanking Active TSS	Liver	Liver
45	chr12:51417400-51418200	Flanking Active TSS	Brain Substantia Nigra	brain
46	chr12:51417400-51418200	Enhancers	Colon Smooth Muscle	Colon
47	chr12:51417400-51418200	Flanking Active TSS	Hela-S3	cervix
48	chr12:51417400-51418400	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr12:51417400-51418600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:51417400-51420600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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