Variant report

Variant	rs1720068
Chromosome Location	chr12:122363695-122363696
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122363070..122365910-chr12:122708968..122710570,2	MCF-7	breast:
2	chr12:122363293..122365854-chr12:122367489..122369682,2	K562	blood:
3	chr12:122362990..122366186-chr12:122458402..122460997,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110987	Chromatin interaction
ENSG00000184047	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1154517	0.86[YRI][hapmap]
rs1168658	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168661	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1169076	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs1169081	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1169084	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1169091	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs1177588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs1179947	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs12578258	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579389	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12579730	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1375653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs1375654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1375655	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs14259	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1630699	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs1667586	0.83[ASN][1000 genomes]
rs1678952	1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.83[ASN][1000 genomes]
rs1678953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs1720030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs1720066	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17852561	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2009257	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2272133	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs2272135	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309275	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2442439	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2688409	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35252940	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3825172	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4069666	0.95[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4760108	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs482421	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs483416	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs508395	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529736	0.81[YRI][hapmap]
rs55826938	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56177852	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58379261	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59517025	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59972569	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs686220	0.83[ASN][1000 genomes]
rs7309105	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7313748	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs745327	0.82[CHB][hapmap]
rs830115	0.80[EUR][1000 genomes]
rs830121	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs876934	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122355600-122364800	Weak transcription	K562	blood
2	chr12:122357000-122370200	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122357000-122370600	Weak transcription	Aorta	Aorta
4	chr12:122357000-122380400	Weak transcription	Gastric	stomach
5	chr12:122357000-122383600	Weak transcription	Primary T cells from cord blood	blood
6	chr12:122359600-122364600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:122359600-122364800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr12:122360000-122364400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr12:122360600-122364800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:122361600-122365400	Weak transcription	Brain Substantia Nigra	brain
11	chr12:122361600-122366000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:122362000-122364600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr12:122362200-122364600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:122362600-122363800	Enhancers	Fetal Stomach	stomach
15	chr12:122362800-122363800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr12:122362800-122364600	Weak transcription	GM12878-XiMat	blood
17	chr12:122363000-122363800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:122363000-122384800	Weak transcription	Psoas Muscle	Psoas
19	chr12:122363000-122393400	Weak transcription	Brain Angular Gyrus	brain
20	chr12:122363200-122365600	Weak transcription	Hela-S3	cervix
21	chr12:122363200-122384600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:122363400-122363800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr12:122363400-122363800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:122363400-122363800	Enhancers	HSMM	muscle
25	chr12:122363400-122363800	Flanking Active TSS	NHDF-Ad	bronchial
26	chr12:122363400-122363800	Enhancers	NHEK	skin
27	chr12:122363400-122364000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:122363400-122364000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:122363400-122364400	Enhancers	Fetal Muscle Leg	muscle
30	chr12:122363400-122364800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:122363400-122364800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:122363400-122364800	Weak transcription	HMEC	breast
33	chr12:122363400-122365600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr12:122363400-122369600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:122363400-122372000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:122363400-122375000	Weak transcription	Spleen	Spleen
37	chr12:122363400-122377000	Weak transcription	Fetal Intestine Small	intestine
38	chr12:122363600-122363800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:122363600-122363800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr12:122363600-122363800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:122363600-122363800	Enhancers	Adipose Nuclei	Adipose
42	chr12:122363600-122363800	Enhancers	Fetal Muscle Trunk	muscle
43	chr12:122363600-122363800	Enhancers	HSMMtube	muscle
44	chr12:122363600-122363800	Enhancers	NHLF	lung
45	chr12:122363600-122364600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:122363600-122364600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:122363600-122364600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr12:122363600-122364800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:122363600-122364800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:122363600-122364800	Weak transcription	Lung	lung

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