Variant report

Variant	rs11560820
Chromosome Location	chr12:123966973-123966974
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	chr12:123963175..123966978-chr12:123967534..123970202,4	MCF-7	breast:
2	chr12:123965117..123967969-chr12:123974414..123976092,3	K562	blood:

Variant related genes	Relation type
ENSG00000188026	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11497308	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11497312	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11497313	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11507739	1.00[ASN][1000 genomes]
rs11507744	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11516176	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11516178	1.00[ASN][1000 genomes]
rs11522340	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11526043	0.82[EUR][1000 genomes]
rs11534428	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11559494	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13303266	1.00[ASN][1000 genomes]
rs13303358	1.00[ASN][1000 genomes]
rs28483351	1.00[ASN][1000 genomes]
rs28613273	1.00[ASN][1000 genomes]
rs28728075	1.00[ASN][1000 genomes]
rs28829651	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087496	1.00[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34031619	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35322317	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4047517	1.00[ASN][1000 genomes]
rs4078291	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4479070	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6606747	1.00[CEU][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300562	1.00[ASN][1000 genomes]
rs7315901	1.00[ASN][1000 genomes]
rs73412280	1.00[ASN][1000 genomes]
rs7975636	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978323	1.00[ASN][1000 genomes]
rs9330649	1.00[ASN][1000 genomes]
rs9330650	1.00[ASN][1000 genomes]
rs9697264	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9697459	1.00[ASN][1000 genomes]
rs9697616	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9697628	1.00[ASN][1000 genomes]
rs9697735	1.00[ASN][1000 genomes]
rs9723046	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9723192	1.00[ASN][1000 genomes]
rs9777813	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9778112	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1822004	chr12:123919287-124013451	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1037260	chr12:123956749-124023069	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123944600-123995600	Weak transcription	Hela-S3	cervix
2	chr12:123944600-124012200	Strong transcription	Fetal Stomach	stomach
3	chr12:123947600-123971800	Strong transcription	Fetal Intestine Small	intestine
4	chr12:123949000-123984400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:123950400-123973000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:123950800-124007600	Weak transcription	Colonic Mucosa	Colon
7	chr12:123953800-123968200	Weak transcription	GM12878-XiMat	blood
8	chr12:123954200-123971000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr12:123955200-123971000	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr12:123956800-123973400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:123956800-123993400	Weak transcription	HMEC	breast
12	chr12:123956800-123995400	Weak transcription	Fetal Brain Male	brain
13	chr12:123957400-123968200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:123957400-123968400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:123957400-123972800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:123957400-123973000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:123957400-123982400	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:123957400-123995400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:123957400-123995400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:123957600-123967800	Weak transcription	Dnd41	blood
21	chr12:123957600-123968200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:123957600-123995400	Weak transcription	Pancreas	Pancrea
23	chr12:123957600-124003800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:123957800-123967600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:123957800-123982600	Weak transcription	A549	lung
26	chr12:123959000-123970400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:123959400-123970600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:123959800-123968200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:123960000-123995400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:123960200-123968200	Weak transcription	Primary T cells from cord blood	blood
31	chr12:123960200-123968200	Weak transcription	Thymus	Thymus
32	chr12:123960200-123972200	Weak transcription	Fetal Kidney	kidney
33	chr12:123960200-123973000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:123960400-123967000	Weak transcription	Primary B cells from cord blood	blood
35	chr12:123960400-123968000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:123960400-123968000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:123960400-123968200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:123960400-123968200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:123960400-123968400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:123961400-123969600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:123961600-123968000	Weak transcription	Liver	Liver
42	chr12:123961600-123973200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr12:123961600-123979200	Weak transcription	NHEK	skin
44	chr12:123961600-123995800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:123963000-123981200	Weak transcription	Esophagus	oesophagus
46	chr12:123963400-123968400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:123963800-123970400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr12:123964000-123967000	Weak transcription	Ovary	ovary
49	chr12:123964000-123978600	Weak transcription	Right Atrium	heart
50	chr12:123964200-123967800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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