Variant report

Variant	rs12369505
Chromosome Location	chr12:49277050-49277051
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49246388..49252218-chr12:49276087..49280065,7	MCF-7	breast:
2	chr12:49275956..49279461-chr12:49283300..49286531,4	MCF-7	breast:
3	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
4	chr12:49253541..49263542-chr12:49271204..49284916,35	MCF-7	breast:
5	chr12:49275330..49277454-chr12:49281174..49283027,2	MCF-7	breast:
6	chr12:49275988..49277601-chr12:49279454..49281035,2	MCF-7	breast:
7	chr12:49270319..49273192-chr12:49274654..49277123,3	MCF-7	breast:
8	chr12:49244448..49248825-chr12:49273797..49278851,6	MCF-7	breast:
9	chr12:49276917..49280280-chr12:49283219..49286162,3	K562	blood:
10	chr12:49265197..49267414-chr12:49276769..49280973,3	MCF-7	breast:
11	chr12:49275988..49277581-chr12:49412229..49413782,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000174243	Chromatin interaction
ENSG00000199394	Chromatin interaction
ENSG00000181929	Chromatin interaction
ENSG00000172602	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10747556	0.86[CHB][hapmap]
rs10747557	0.84[CHB][hapmap]
rs10747558	0.82[CHB][hapmap]
rs10783287	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs10783289	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10875883	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs10875885	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11168773	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11168784	0.80[CHB][hapmap]
rs1830192	0.80[CHB][hapmap]
rs2030900	0.80[CHB][hapmap]
rs2070940	0.80[CHB][hapmap]
rs2131713	0.80[CHB][hapmap]
rs2272312	0.80[CHB][hapmap]
rs2293449	0.80[CHB][hapmap]
rs2446985	0.91[ASN][1000 genomes]
rs2446986	0.94[ASN][1000 genomes]
rs2446987	0.97[ASN][1000 genomes]
rs2446999	0.85[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs2447000	0.99[ASN][1000 genomes]
rs2447001	1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[ASN][1000 genomes]
rs2453476	0.96[ASN][1000 genomes]
rs2926806	0.85[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2934998	0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs3958875	0.95[ASN][1000 genomes]
rs4237854	0.80[CHB][hapmap]
rs4433614	0.80[CHB][hapmap]
rs4760647	0.91[ASN][1000 genomes]
rs4760667	0.85[CHB][hapmap]
rs833476	0.98[ASN][1000 genomes]
rs833478	0.97[ASN][1000 genomes]
rs833479	0.97[ASN][1000 genomes]
rs833483	0.85[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs833484	0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49271400-49278200	Enhancers	Liver	Liver
2	chr12:49274000-49278800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:49275000-49278600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:49275200-49278200	Enhancers	Fetal Intestine Large	intestine
5	chr12:49275200-49278200	Enhancers	Fetal Intestine Small	intestine
6	chr12:49275400-49277800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:49275400-49278200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:49275600-49277200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr12:49275600-49277200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:49275600-49277400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:49275600-49277600	Bivalent Enhancer	Fetal Muscle Leg	muscle
12	chr12:49275600-49277800	Enhancers	Placenta	Placenta
13	chr12:49275600-49278000	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:49275600-49278000	Enhancers	Fetal Lung	lung
15	chr12:49275600-49278000	Enhancers	Lung	lung
16	chr12:49275600-49278000	Enhancers	Pancreas	Pancrea
17	chr12:49275600-49278200	Flanking Active TSS	A549	lung
18	chr12:49275800-49277200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:49275800-49277200	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:49275800-49278000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:49275800-49278000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:49275800-49278000	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:49275800-49278200	Enhancers	H1 Cell Line	embryonic stem cell
24	chr12:49275800-49278200	Enhancers	Brain Angular Gyrus	brain
25	chr12:49275800-49278200	Enhancers	Fetal Brain Male	brain
26	chr12:49275800-49278200	Enhancers	K562	blood
27	chr12:49276000-49277400	Enhancers	Brain Cingulate Gyrus	brain
28	chr12:49276000-49277400	Enhancers	Brain Germinal Matrix	brain
29	chr12:49276000-49277600	Enhancers	Fetal Muscle Trunk	muscle
30	chr12:49276000-49277800	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:49276000-49277800	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr12:49276000-49278000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:49276000-49278000	Enhancers	Fetal Brain Female	brain
34	chr12:49276000-49278200	Bivalent Enhancer	Fetal Stomach	stomach
35	chr12:49276200-49277400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:49276200-49278000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:49276200-49278400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:49276400-49277400	Bivalent Enhancer	NHLF	lung
39	chr12:49276400-49277800	Enhancers	Right Atrium	heart
40	chr12:49276400-49278000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:49276400-49278200	Enhancers	H9 Cell Line	embryonic stem cell
42	chr12:49276400-49278200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr12:49276400-49278400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr12:49276600-49277200	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr12:49276600-49277400	Weak transcription	Left Ventricle	heart
46	chr12:49276600-49277800	Enhancers	Adipose Nuclei	Adipose
47	chr12:49276600-49278000	Enhancers	Fetal Kidney	kidney
48	chr12:49276600-49278200	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:49276600-49278400	Enhancers	Stomach Mucosa	stomach
50	chr12:49276800-49277200	Flanking Bivalent TSS/Enh	HepG2	liver

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