Variant report

Variant	rs6486794
Chromosome Location	chr12:122469878-122469879
allele	C/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122468999..122472333-chr12:122516550..122518096,3	MCF-7	breast:
2	chr12:122355526..122356732-chr12:122469218..122470177,3	MCF-7	breast:
3	chr12:122469175..122470175-chr12:122675088..122676086,5	K562	blood:
4	chr12:122469735..122472102-chr12:122500091..122502087,2	K562	blood:
5	chr12:122366146..122368604-chr12:122467424..122470233,2	MCF-7	breast:
6	chr12:122394265..122395832-chr12:122468104..122470419,2	MCF-7	breast:
7	chr12:122239067..122243292-chr12:122466352..122470138,4	MCF-7	breast:
8	chr12:122393339..122394256-chr12:122469215..122470133,3	MCF-7	breast:
9	chr12:122467922..122470622-chr12:122594628..122596411,2	MCF-7	breast:
10	chr12:122469231..122471324-chr12:122480091..122482011,2	MCF-7	breast:
11	chr12:122468573..122470930-chr12:122610442..122612182,2	MCF-7	breast:
12	chr12:122390662..122395297-chr12:122466472..122469968,4	MCF-7	breast:
13	chr12:122241638..122243291-chr12:122468196..122471069,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139718	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1154510	0.82[CEU][hapmap];0.80[MEX][hapmap]
rs1154513	0.81[AMR][1000 genomes]
rs1169075	0.90[AMR][1000 genomes]
rs1169077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1169080	0.86[AMR][1000 genomes]
rs1169082	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1169085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1169092	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1169093	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1182927	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1185260	0.82[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs1667583	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap]
rs1667584	0.81[AMR][1000 genomes]
rs1678969	0.83[JPT][hapmap]
rs1720041	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1916333	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2230681	0.82[CEU][hapmap]
rs2247291	0.82[CEU][hapmap]
rs2596144	0.82[CEU][hapmap]
rs2620340	0.82[CEU][hapmap]
rs2707056	0.82[CEU][hapmap]
rs4760099	0.82[CEU][hapmap]
rs493519	0.82[CEU][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes]
rs529736	0.86[MEX][hapmap]
rs693277	0.81[AMR][1000 genomes]
rs7314056	0.82[CEU][hapmap];0.85[MEX][hapmap]
rs7957207	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961103	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs830116	0.81[AMR][1000 genomes]
rs830120	0.90[MEX][hapmap]
rs830122	1.00[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs830123	1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs830124	0.82[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs830126	0.84[AMR][1000 genomes]
rs853758	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs895958	0.82[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs895959	0.82[CEU][hapmap]
rs9739533	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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	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	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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122461600-122492400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:122461800-122473200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:122461800-122476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:122462000-122473200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:122462000-122473400	Weak transcription	Primary T cells from cord blood	blood
6	chr12:122462000-122492400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr12:122462200-122472800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:122462200-122473000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:122462200-122473200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:122462200-122473400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:122462200-122474200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr12:122462200-122489000	Weak transcription	HUVEC	blood vessel
13	chr12:122462400-122470000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:122462400-122473200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:122462400-122473200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:122462400-122473200	Weak transcription	Aorta	Aorta
17	chr12:122462400-122473200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:122462400-122477800	Weak transcription	Fetal Kidney	kidney
19	chr12:122462400-122481800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:122462400-122489000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:122462400-122490400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:122462400-122492200	Weak transcription	Stomach Mucosa	stomach
23	chr12:122462400-122500000	Weak transcription	Hela-S3	cervix
24	chr12:122462600-122478000	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:122462800-122473000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr12:122463200-122470000	Enhancers	Primary B cells from cord blood	blood
27	chr12:122464400-122470600	Enhancers	Pancreas	Pancrea
28	chr12:122465200-122473200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:122465600-122470200	Enhancers	Left Ventricle	heart
30	chr12:122465600-122470800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr12:122465800-122470200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:122466200-122500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:122466400-122473600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:122466400-122489000	Weak transcription	NHLF	lung
35	chr12:122466800-122472800	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:122466800-122490200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:122467000-122472800	Weak transcription	Adipose Nuclei	Adipose
38	chr12:122467000-122480600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr12:122467200-122472600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:122467200-122472800	Weak transcription	Brain Angular Gyrus	brain
41	chr12:122467200-122472800	Weak transcription	Brain Germinal Matrix	brain
42	chr12:122467400-122472800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:122467400-122473200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:122467800-122472400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:122467800-122472800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr12:122467800-122473000	Weak transcription	Brain Anterior Caudate	brain
47	chr12:122467800-122473200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:122467800-122478000	Strong transcription	Fetal Intestine Small	intestine
49	chr12:122467800-122488800	Weak transcription	Right Atrium	heart
50	chr12:122467800-122500000	Strong transcription	Thymus	Thymus

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