Variant report

Variant	rs17120038
Chromosome Location	chr12:58344857-58344858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58339956..58342455-chr12:58344235..58346244,2	MCF-7	breast:
2	chr12:58335319..58338203-chr12:58340129..58346317,10	K562	blood:
3	chr12:58343666..58345646-chr12:58346794..58349632,2	MCF-7	breast:
4	chr12:58334540..58337378-chr12:58339251..58345306,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166896	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12816216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827346	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12829858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830273	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12831787	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120058	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120201	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888286	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2888287	0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34080411	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34142683	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34170251	0.96[ASN][1000 genomes]
rs34221389	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34238095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34300531	0.96[ASN][1000 genomes]
rs34437870	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34499234	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34567504	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35326083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364486	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35375157	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35712620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35726562	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56964775	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61015952	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61935800	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61935801	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581160	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581162	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581163	0.80[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132343	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137226	0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs7295307	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];1.00[ASN][1000 genomes]
rs7299512	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307628	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962775	0.82[JPT][hapmap]
rs7968265	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970948	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971139	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7978519	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58336000-58345200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:58336000-58347600	Weak transcription	Esophagus	oesophagus
3	chr12:58336000-58348400	Weak transcription	Gastric	stomach
4	chr12:58336000-58348600	Weak transcription	Aorta	Aorta
5	chr12:58336000-58348600	Weak transcription	Lung	lung
6	chr12:58336000-58351000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr12:58336000-58351000	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:58336000-58351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:58336000-58351200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:58336000-58351200	Weak transcription	Spleen	Spleen
11	chr12:58336000-58353000	Weak transcription	Small Intestine	intestine
12	chr12:58336200-58345000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:58336200-58346600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:58336200-58346600	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:58336200-58347600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:58336200-58350600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:58336200-58350600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:58336200-58350800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:58336200-58351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:58336200-58351000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr12:58336200-58351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:58336200-58351200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:58336200-58351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:58336200-58351200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:58336200-58351200	Weak transcription	Fetal Intestine Small	intestine
26	chr12:58336200-58351200	Weak transcription	Placenta	Placenta
27	chr12:58336200-58351400	Weak transcription	Brain Anterior Caudate	brain
28	chr12:58336200-58351400	Weak transcription	Fetal Lung	lung
29	chr12:58336200-58351600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr12:58336200-58351600	Weak transcription	HUVEC	blood vessel
31	chr12:58336200-58353000	Weak transcription	Stomach Mucosa	stomach
32	chr12:58336200-58353400	Weak transcription	Fetal Kidney	kidney
33	chr12:58336200-58353600	Weak transcription	Brain Substantia Nigra	brain
34	chr12:58336200-58353600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:58336200-58353800	Weak transcription	Brain Angular Gyrus	brain
36	chr12:58336200-58353800	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:58336200-58354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:58336200-58354000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:58336200-58354000	Weak transcription	Psoas Muscle	Psoas
40	chr12:58336200-58356200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:58336200-58359600	Weak transcription	A549	lung
42	chr12:58336400-58351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:58336400-58351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:58336400-58351200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr12:58336400-58359600	Weak transcription	HMEC	breast
46	chr12:58336800-58345200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr12:58336800-58346600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr12:58336800-58351200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:58336800-58353000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:58337000-58350600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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