Variant report

Variant	rs11169042
Chromosome Location	chr12:49870964-49870965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49869107..49872803-chr12:49881863..49884172,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10875952	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs1248365	0.96[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs1248366	0.96[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap]
rs7488783	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 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	chr12:49823000-49915800	Weak transcription	Primary B cells from cord blood	blood
2	chr12:49823400-49876000	Weak transcription	Osteobl	bone
3	chr12:49839200-49876000	Weak transcription	Fetal Thymus	thymus
4	chr12:49840200-49900600	Weak transcription	Pancreas	Pancrea
5	chr12:49840600-49875800	Weak transcription	Hela-S3	cervix
6	chr12:49846000-49879800	Weak transcription	Fetal Lung	lung
7	chr12:49846400-49878400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:49849400-49875800	Weak transcription	HepG2	liver
9	chr12:49850400-49876000	Weak transcription	Fetal Intestine Large	intestine
10	chr12:49850400-49876000	Weak transcription	Small Intestine	intestine
11	chr12:49850400-49878800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:49850400-49911000	Weak transcription	K562	blood
13	chr12:49850600-49876200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:49853200-49876000	Weak transcription	HSMMtube	muscle
15	chr12:49853200-49913400	Weak transcription	Thymus	Thymus
16	chr12:49854400-49878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:49855200-49872600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:49856400-49872600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:49856400-49883400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:49856600-49872800	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:49856600-49874400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:49856600-49875800	Weak transcription	Adipose Nuclei	Adipose
23	chr12:49856600-49890200	Weak transcription	Primary T cells from cord blood	blood
24	chr12:49856600-49890200	Weak transcription	Ovary	ovary
25	chr12:49856800-49872600	Weak transcription	NHEK	skin
26	chr12:49856800-49876000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:49856800-49876000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:49856800-49876000	Weak transcription	HSMM	muscle
29	chr12:49856800-49876200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:49856800-49883600	Weak transcription	Dnd41	blood
31	chr12:49856800-49898400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:49857000-49876000	Weak transcription	NH-A	brain
33	chr12:49858200-49875800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:49859200-49876000	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:49859400-49883400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr12:49859400-49888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:49865000-49872800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:49865200-49876000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:49865600-49872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:49865600-49875600	Weak transcription	A549	lung
41	chr12:49865800-49875800	Weak transcription	HMEC	breast
42	chr12:49867200-49876000	Weak transcription	Psoas Muscle	Psoas
43	chr12:49867800-49872800	Weak transcription	Right Ventricle	heart
44	chr12:49867800-49875400	Weak transcription	HUVEC	blood vessel
45	chr12:49868000-49872400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr12:49869000-49872800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:49869400-49876200	Weak transcription	Brain Germinal Matrix	brain
48	chr12:49869600-49890000	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr12:49869600-49918400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:49870000-49877600	Weak transcription	GM12878-XiMat	blood

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