Variant report

Variant	rs6581163
Chromosome Location	chr12:58348425-58348426
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58335462..58338789-chr12:58345591..58348596,3	MCF-7	breast:
2	chr12:58331126..58336809-chr12:58347198..58351955,8	K562	blood:
3	chr12:58347570..58349774-chr12:58354574..58356685,2	MCF-7	breast:
4	chr12:58343666..58345646-chr12:58346794..58349632,2	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];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822306	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827346	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12829858	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830273	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12831787	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120038	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]
rs17120048	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120057	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120058	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120198	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17120201	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120203	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2888286	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2888287	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34080411	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34142683	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34170251	0.96[ASN][1000 genomes]
rs34221389	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34238095	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34300531	0.96[ASN][1000 genomes]
rs34437870	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34499234	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34567504	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35326083	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35364486	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35375157	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35712620	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35726562	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829337	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56964775	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61015952	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61935800	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61935801	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581160	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581162	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132343	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133275	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7136078	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7137226	0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs7295307	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][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]
rs7299512	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303136	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307628	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962775	0.82[JPT][hapmap]
rs7968265	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7970948	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971139	0.86[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:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58336000-58348600	Weak transcription	Aorta	Aorta
2	chr12:58336000-58348600	Weak transcription	Lung	lung
3	chr12:58336000-58351000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:58336000-58351000	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:58336000-58351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:58336000-58351200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr12:58336000-58351200	Weak transcription	Spleen	Spleen
8	chr12:58336000-58353000	Weak transcription	Small Intestine	intestine
9	chr12:58336200-58350600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:58336200-58350600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:58336200-58350800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:58336200-58351000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:58336200-58351000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:58336200-58351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr12:58336200-58351200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:58336200-58351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:58336200-58351200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:58336200-58351200	Weak transcription	Fetal Intestine Small	intestine
19	chr12:58336200-58351200	Weak transcription	Placenta	Placenta
20	chr12:58336200-58351400	Weak transcription	Brain Anterior Caudate	brain
21	chr12:58336200-58351400	Weak transcription	Fetal Lung	lung
22	chr12:58336200-58351600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:58336200-58351600	Weak transcription	HUVEC	blood vessel
24	chr12:58336200-58353000	Weak transcription	Stomach Mucosa	stomach
25	chr12:58336200-58353400	Weak transcription	Fetal Kidney	kidney
26	chr12:58336200-58353600	Weak transcription	Brain Substantia Nigra	brain
27	chr12:58336200-58353600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:58336200-58353800	Weak transcription	Brain Angular Gyrus	brain
29	chr12:58336200-58353800	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:58336200-58354000	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:58336200-58354000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr12:58336200-58354000	Weak transcription	Psoas Muscle	Psoas
33	chr12:58336200-58356200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:58336200-58359600	Weak transcription	A549	lung
35	chr12:58336400-58351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:58336400-58351000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:58336400-58351200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr12:58336400-58359600	Weak transcription	HMEC	breast
39	chr12:58336800-58351200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr12:58336800-58353000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:58337000-58350600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:58337200-58350600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:58337200-58351000	Weak transcription	Colonic Mucosa	Colon
44	chr12:58337200-58358400	Weak transcription	HepG2	liver
45	chr12:58337600-58350600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:58337800-58349400	Weak transcription	GM12878-XiMat	blood
47	chr12:58339600-58352200	Strong transcription	Primary T cells from cord blood	blood
48	chr12:58340000-58350600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:58340000-58351600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr12:58340200-58351400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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