Variant report

Variant	rs645661
Chromosome Location	chr12:121316110-121316111
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121313800..121316654-chr12:121341706..121344079,2	MCF-7	breast:
2	chr12:121315603..121319201-chr12:121319262..121323037,3	K562	blood:

Variant related genes	Relation type
ENSG00000157837	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1055059	1.00[ASN][1000 genomes]
rs10849777	1.00[ASN][1000 genomes]
rs10849797	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065201	1.00[ASN][1000 genomes]
rs11065207	1.00[ASN][1000 genomes]
rs11065210	1.00[ASN][1000 genomes]
rs11065213	1.00[GIH][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs11065226	1.00[ASN][1000 genomes]
rs11065227	1.00[ASN][1000 genomes]
rs11065228	1.00[ASN][1000 genomes]
rs11065253	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11065254	1.00[ASN][1000 genomes]
rs11065258	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11065260	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11065267	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11065275	0.86[CEU][hapmap];1.00[ASN][1000 genomes]
rs11065279	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs11065281	0.84[EUR][1000 genomes]
rs11065285	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065286	0.85[YRI][hapmap]
rs11065288	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065291	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065294	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065308	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065309	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065315	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065318	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065326	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065328	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065334	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11065347	1.00[ASN][1000 genomes]
rs11065353	1.00[ASN][1000 genomes]
rs1151854	0.82[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151855	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151860	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1151865	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1186042	1.00[ASN][1000 genomes]
rs12366451	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs12368617	1.00[ASN][1000 genomes]
rs12370534	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696358	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1696362	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs1718207	1.00[ASN][1000 genomes]
rs1732397	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732399	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2454728	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2701179	1.00[ASN][1000 genomes]
rs497457	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs498255	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs513940	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs515784	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519785	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs530162	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs554197	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs572009	1.00[ASN][1000 genomes]
rs574993	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581515	0.91[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs582678	1.00[CEU][hapmap];0.89[YRI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs590556	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591489	1.00[ASN][1000 genomes]
rs59818945	1.00[ASN][1000 genomes]
rs61108232	1.00[ASN][1000 genomes]
rs61414515	1.00[ASN][1000 genomes]
rs61624288	1.00[ASN][1000 genomes]
rs627211	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs639343	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs645786	1.00[ASN][1000 genomes]
rs647336	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648262	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs651156	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660878	1.00[ASN][1000 genomes]
rs671815	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];1.00[ASN][1000 genomes]
rs708784	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs708788	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs73409953	1.00[ASN][1000 genomes]
rs73411916	1.00[ASN][1000 genomes]
rs73413866	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73413874	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960932	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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763007	chr12:121309851-121317278	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121288000-121316600	Weak transcription	NHLF	lung
2	chr12:121288200-121339600	Weak transcription	Hela-S3	cervix
3	chr12:121294200-121340400	Weak transcription	HSMM	muscle
4	chr12:121295000-121316200	Weak transcription	HMEC	breast
5	chr12:121297400-121339800	Weak transcription	A549	lung
6	chr12:121300600-121328800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:121302000-121328800	Weak transcription	Fetal Intestine Large	intestine
8	chr12:121304200-121329800	Weak transcription	K562	blood
9	chr12:121304600-121339800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:121304800-121322000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:121304800-121324200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:121305000-121317400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:121306000-121322800	Weak transcription	Primary B cells from cord blood	blood
14	chr12:121306200-121319800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:121306600-121326600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:121306600-121331400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:121308600-121316200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:121308800-121316600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:121308800-121323200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:121309200-121317000	Weak transcription	NHEK	skin
21	chr12:121310400-121317000	Weak transcription	HepG2	liver
22	chr12:121310800-121323600	Weak transcription	Fetal Thymus	thymus
23	chr12:121310800-121331400	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:121311200-121316600	Weak transcription	Liver	Liver
25	chr12:121311200-121322400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:121311200-121323200	Weak transcription	Thymus	Thymus
27	chr12:121311400-121321800	Weak transcription	Primary T cells from cord blood	blood
28	chr12:121311400-121323000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr12:121311400-121323800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:121311600-121317000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:121312000-121323200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:121312000-121323400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:121312000-121323400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:121312600-121317200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:121312600-121339800	Weak transcription	Brain Germinal Matrix	brain
36	chr12:121312600-121339800	Weak transcription	NHDF-Ad	bronchial
37	chr12:121312800-121321600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:121312800-121322800	Weak transcription	GM12878-XiMat	blood
39	chr12:121313000-121316400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:121313000-121317200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:121313000-121317200	Weak transcription	Brain Anterior Caudate	brain
42	chr12:121313000-121321600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:121313000-121322600	Weak transcription	Brain Angular Gyrus	brain
44	chr12:121313000-121322800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:121313000-121323200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:121313000-121323400	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr12:121313000-121325800	Weak transcription	Ovary	ovary
48	chr12:121313000-121332600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:121313200-121317200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr12:121313400-121317400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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