Variant report

Variant	rs11111858
Chromosome Location	chr12:104357682-104357683
allele	A/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:2)
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	chr12:104356512..104358461-chr12:104416021..104418355,2	K562	blood:
2	chr12:104323659..104328405-chr12:104357607..104360751,5	MCF-7	breast:
3	chr12:104357292..104359018-chr12:104494120..104496296,2	MCF-7	breast:
4	chr12:104319225..104328292-chr12:104356282..104362179,14	K562	blood:
5	chr12:104356409..104362053-chr12:104528975..104533138,7	MCF-7	breast:
6	chr12:104328917..104332179-chr12:104357230..104361045,4	MCF-7	breast:
7	chr12:104324052..104326463-chr12:104355875..104358112,3	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TDG-1	chr12:104357017-104357920	NONHSAT030400
2	lnc-C12orf73-2	chr12:104357568-104359481	NONHSAT030401

No data

Variant related genes	Relation type
ENSG00000214198	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000120837	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10507172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10507173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861124	1.00[JPT][hapmap]
rs10861147	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10861148	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs10861153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11111817	0.87[JPT][hapmap]
rs11111862	1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs11111863	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11111865	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11111866	0.83[ASN][1000 genomes]
rs1165666	1.00[JPT][hapmap]
rs1165677	1.00[JPT][hapmap]
rs1165678	1.00[JPT][hapmap]
rs1165682	1.00[JPT][hapmap]
rs1183212	1.00[JPT][hapmap]
rs12368121	1.00[JPT][hapmap]
rs12368164	1.00[JPT][hapmap]
rs1437502	0.90[ASN][1000 genomes]
rs17035144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1866070	1.00[JPT][hapmap]
rs2164747	1.00[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs2251979	0.87[JPT][hapmap]
rs2252000	0.89[JPT][hapmap]
rs2293620	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2438116	1.00[JPT][hapmap]
rs2722188	0.87[JPT][hapmap]
rs3751210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3817602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3829301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs4135051	1.00[CEU][hapmap]
rs4135052	1.00[ASN][1000 genomes]
rs4135054	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4135068	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs4135079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4135102	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4135103	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4135109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4135113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4135115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4135126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57179875	0.95[ASN][1000 genomes]
rs60696717	0.93[ASN][1000 genomes]
rs61069788	0.90[ASN][1000 genomes]
rs6539104	0.87[JPT][hapmap]
rs7137924	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7295650	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7302074	1.00[JPT][hapmap]
rs7305770	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7310423	0.95[ASN][1000 genomes]
rs73388292	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73390443	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	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
2	nsv427922	chr12:104325583-104523096	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	esv1799879	chr12:104351057-104360713	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104351400-104358000	Weak transcription	Lung	lung
2	chr12:104351400-104358000	Weak transcription	Spleen	Spleen
3	chr12:104351600-104357800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:104351600-104357800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:104351600-104357800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr12:104351600-104357800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr12:104351600-104357800	Weak transcription	HSMMtube	muscle
8	chr12:104351600-104357800	Weak transcription	NHDF-Ad	bronchial
9	chr12:104351600-104357800	Weak transcription	NHEK	skin
10	chr12:104351600-104357800	Weak transcription	Osteobl	bone
11	chr12:104351600-104358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:104351600-104358000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:104351600-104358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:104351600-104358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr12:104351600-104358000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:104351600-104358000	Weak transcription	Esophagus	oesophagus
17	chr12:104351600-104358000	Weak transcription	Fetal Intestine Small	intestine
18	chr12:104351600-104358000	Weak transcription	Ovary	ovary
19	chr12:104351600-104358000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:104351600-104358000	Weak transcription	Right Ventricle	heart
21	chr12:104351600-104358000	Weak transcription	Thymus	Thymus
22	chr12:104351600-104358000	Weak transcription	HMEC	breast
23	chr12:104351600-104358200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:104351600-104358200	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:104351600-104358200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:104351600-104358200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:104351600-104358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:104351600-104358200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:104351600-104358200	Weak transcription	Aorta	Aorta
30	chr12:104351600-104358200	Weak transcription	Brain Anterior Caudate	brain
31	chr12:104351600-104358200	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:104351600-104358200	Weak transcription	Fetal Stomach	stomach
33	chr12:104351600-104358400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:104351600-104358400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr12:104351800-104358200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:104352000-104357800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr12:104352000-104357800	Weak transcription	Adipose Nuclei	Adipose
38	chr12:104352000-104357800	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:104352000-104358000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr12:104352000-104358000	Weak transcription	Left Ventricle	heart
41	chr12:104352000-104358400	Weak transcription	Primary B cells from cord blood	blood
42	chr12:104352200-104358200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:104352600-104357800	Weak transcription	HSMM	muscle
44	chr12:104352600-104358000	Weak transcription	Liver	Liver
45	chr12:104352600-104358000	Weak transcription	HUVEC	blood vessel
46	chr12:104353000-104357800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:104353000-104357800	Weak transcription	Dnd41	blood
48	chr12:104353000-104358200	Weak transcription	Hela-S3	cervix
49	chr12:104353200-104357800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:104354200-104357800	Weak transcription	H1 Cell Line	embryonic stem cell

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