Variant report

Variant	rs12281438
Chromosome Location	chr11:45179117-45179118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45164428..45170441-chr11:45176063..45179885,12	MCF-7	breast:
2	chr11:45176255..45180138-chr11:45180420..45184771,5	MCF-7	breast:
3	chr11:45178718..45181474-chr11:45186088..45187942,2	K562	blood:
4	chr11:45175116..45179672-chr11:45200428..45203177,5	MCF-7	breast:
5	chr11:45166948..45170773-chr11:45176737..45181280,4	K562	blood:
6	chr11:45173226..45176543-chr11:45176880..45179156,4	K562	blood:

Variant related genes	Relation type
ENSG00000019485	Chromatin interaction

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

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

rs_ID	r²[population]
rs10742743	0.86[JPT][hapmap]
rs10742744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742745	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10742746	0.87[ASN][1000 genomes]
rs1078930	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838425	0.86[JPT][hapmap]
rs10838426	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11038356	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11038361	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2863159	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs3758722	1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3758728	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781706	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4755948	0.95[EUR][1000 genomes]
rs4755953	0.86[JPT][hapmap]
rs6416128	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6485594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485596	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485597	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6485598	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6485599	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6485601	0.95[EUR][1000 genomes]
rs6485602	1.00[CEU][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs746555	0.95[EUR][1000 genomes]
rs7937949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7942214	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7942347	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7945018	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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	nsv825852	chr11:45141386-45228580	Bivalent/Poised TSS Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv541025	chr11:45154352-45193352	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv1048493	chr11:45166054-45205695	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv523057	chr11:45174530-45181682	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45169400-45181600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr11:45169800-45188000	Weak transcription	Primary T cells from cord blood	blood
3	chr11:45170000-45179200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:45170000-45179400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr11:45170000-45190000	Weak transcription	Primary B cells from cord blood	blood
6	chr11:45170200-45179200	Weak transcription	Colonic Mucosa	Colon
7	chr11:45170200-45179400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:45170200-45179400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr11:45170400-45179600	Weak transcription	Fetal Brain Female	brain
10	chr11:45170400-45185200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr11:45170600-45179400	Weak transcription	Psoas Muscle	Psoas
12	chr11:45170800-45179600	Weak transcription	Fetal Brain Male	brain
13	chr11:45170800-45180800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr11:45171200-45179200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:45172400-45190000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr11:45174000-45179200	Weak transcription	Stomach Mucosa	stomach
17	chr11:45175400-45182800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:45175600-45186200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr11:45176000-45181400	Enhancers	Right Ventricle	heart
20	chr11:45176000-45181400	Enhancers	Spleen	Spleen
21	chr11:45176000-45181600	Enhancers	Placenta	Placenta
22	chr11:45176000-45184200	Enhancers	Fetal Lung	lung
23	chr11:45176000-45186600	Genic enhancers	Fetal Stomach	stomach
24	chr11:45176200-45179600	Enhancers	HepG2	liver
25	chr11:45176200-45181800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr11:45176600-45183600	Enhancers	Esophagus	oesophagus
27	chr11:45177000-45179200	Weak transcription	Adipose Nuclei	Adipose
28	chr11:45177000-45179800	Weak transcription	Aorta	Aorta
29	chr11:45177400-45180400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr11:45177600-45179200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:45177800-45180800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:45178000-45179200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:45178200-45181200	Enhancers	Ovary	ovary
34	chr11:45178200-45183600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:45178200-45187600	Enhancers	Fetal Heart	heart
36	chr11:45178400-45179200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:45178400-45179200	Genic enhancers	Fetal Muscle Trunk	muscle
38	chr11:45178400-45179600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr11:45178400-45180000	Enhancers	Colon Smooth Muscle	Colon
40	chr11:45178400-45181000	Enhancers	Duodenum Mucosa	Duodenum
41	chr11:45178400-45181400	Enhancers	Right Atrium	heart
42	chr11:45178400-45181800	Enhancers	Left Ventricle	heart
43	chr11:45178400-45185200	Enhancers	Fetal Muscle Leg	muscle
44	chr11:45178600-45179200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr11:45178600-45179800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr11:45178600-45180600	Enhancers	Pancreas	Pancrea
47	chr11:45178600-45180600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr11:45178600-45181000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr11:45178600-45181200	Enhancers	Brain Anterior Caudate	brain
50	chr11:45178600-45181800	Enhancers	Lung	lung

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