Variant report

Variant	rs10880859
Chromosome Location	chr12:46195849-46195850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46192311..46194076-chr12:46195013..46197310,2	MCF-7	breast:
2	chr12:46195732..46198706-chr12:46294944..46297552,2	MCF-7	breast:
3	chr12:46122269..46124153-chr12:46195545..46198250,2	K562	blood:
4	chr12:46122653..46126469-chr12:46195545..46199194,4	K562	blood:

Variant related genes	Relation type
ENSG00000189079	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10748432	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880855	0.91[EUR][1000 genomes]
rs10880860	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10880864	0.82[EUR][1000 genomes]
rs11183201	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12319077	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12320533	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1468993	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1863127	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059404	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2193749	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2408435	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs247917	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247918	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247919	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247920	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247929	0.81[ASN][1000 genomes]
rs247930	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35115	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35117	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35121	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35122	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35125	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6582574	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67133230	0.86[EUR][1000 genomes]
rs7132422	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7138997	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7955891	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7976870	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	esv2758306	chr12:46149338-46349891	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759897	chr12:46149338-46349891	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv832396	chr12:46155424-46310583	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv3325128	chr12:46175148-46224560	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46132000-46205200	Weak transcription	HSMM	muscle
2	chr12:46149600-46215400	Weak transcription	Fetal Kidney	kidney
3	chr12:46157400-46199600	Weak transcription	HepG2	liver
4	chr12:46164600-46205200	Weak transcription	Dnd41	blood
5	chr12:46164600-46230000	Weak transcription	Thymus	Thymus
6	chr12:46166800-46199800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:46167600-46205200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:46169000-46197600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:46169000-46202400	Weak transcription	Aorta	Aorta
10	chr12:46169000-46202400	Weak transcription	Left Ventricle	heart
11	chr12:46169000-46202400	Weak transcription	Psoas Muscle	Psoas
12	chr12:46169000-46205200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr12:46169000-46208000	Weak transcription	Brain Angular Gyrus	brain
14	chr12:46169000-46215400	Weak transcription	Fetal Lung	lung
15	chr12:46174200-46205000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:46175200-46215400	Weak transcription	Primary B cells from cord blood	blood
17	chr12:46175600-46205200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:46175800-46205200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:46177400-46215000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:46177600-46205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:46177600-46243400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:46179400-46205200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr12:46182000-46205200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:46182600-46230600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:46183200-46205200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:46183200-46205200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr12:46183600-46197600	Weak transcription	NHDF-Ad	bronchial
28	chr12:46183800-46202400	Weak transcription	Right Ventricle	heart
29	chr12:46183800-46215400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:46183800-46243400	Weak transcription	Small Intestine	intestine
31	chr12:46184400-46197600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:46184600-46231200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr12:46184800-46197800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:46185600-46196000	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:46185600-46205200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:46186000-46233400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:46186200-46201600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:46186200-46205200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr12:46186200-46215200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr12:46186200-46215400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:46186800-46205200	Weak transcription	HMEC	breast
42	chr12:46186800-46243400	Weak transcription	HSMMtube	muscle
43	chr12:46187400-46205200	Weak transcription	HUVEC	blood vessel
44	chr12:46188600-46205200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr12:46188800-46205200	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr12:46188800-46205200	Weak transcription	GM12878-XiMat	blood
47	chr12:46189000-46205200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:46189200-46205000	Weak transcription	Primary T cells from cord blood	blood
49	chr12:46189200-46205200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr12:46191400-46215200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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