Variant report

Variant	rs12229292
Chromosome Location	chr12:104153633-104153634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104152829..104155541-chr12:104264505..104266459,2	MCF-7	breast:
2	chr12:104136425..104139178-chr12:104152624..104154639,2	K562	blood:
3	chr12:104141190..104143680-chr12:104152511..104154434,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10861095	0.83[CHB][hapmap]
rs10861096	0.82[CHB][hapmap]
rs10861097	0.82[CHB][hapmap]
rs2271637	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3763993	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3812805	0.82[CHB][hapmap]
rs3817303	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4964830	0.82[CHB][hapmap]
rs4981021	0.86[CEU][hapmap];0.90[AMR][1000 genomes]
rs4981026	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs751448	0.82[CHB][hapmap]
rs869993	0.81[JPT][hapmap]
rs9132	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899486	chr12:104118587-104170474	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv899491	chr12:104151560-104175575	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12229292	RP11-341G23.4	cis	Artery Tibial	GTEx
rs12229292	RP11-341G23.4	cis	Esophagus Muscularis	GTEx
rs12229292	RP11-341G23.4	cis	Thyroid	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104139200-104154200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr12:104140600-104154600	Weak transcription	Aorta	Aorta
3	chr12:104142800-104154600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:104142800-104154600	Weak transcription	NHEK	skin
5	chr12:104145600-104154800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr12:104145800-104166800	Weak transcription	Right Atrium	heart
7	chr12:104146000-104154600	Weak transcription	HSMM	muscle
8	chr12:104146200-104169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:104147000-104159600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:104147000-104165400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr12:104147400-104155800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr12:104148000-104154200	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:104148200-104154400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:104149000-104156800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:104149200-104154200	Weak transcription	A549	lung
16	chr12:104149600-104153800	Weak transcription	Liver	Liver
17	chr12:104150000-104156600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr12:104150000-104166800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:104150600-104154200	Weak transcription	Placenta	Placenta
20	chr12:104150600-104155200	Weak transcription	Fetal Intestine Small	intestine
21	chr12:104151400-104154800	Weak transcription	NH-A	brain
22	chr12:104151400-104158000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:104151600-104155000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr12:104151600-104170400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:104151800-104154800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:104152000-104159800	Weak transcription	Lung	lung
27	chr12:104152400-104154800	Weak transcription	HSMMtube	muscle
28	chr12:104152400-104159400	Weak transcription	Gastric	stomach
29	chr12:104152400-104160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:104152400-104162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:104152400-104162800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:104152600-104154400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:104152600-104158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr12:104152600-104160600	Strong transcription	Spleen	Spleen
35	chr12:104152600-104161600	Strong transcription	HMEC	breast
36	chr12:104152600-104162600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:104152600-104162600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr12:104152600-104162800	Weak transcription	Psoas Muscle	Psoas
39	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
40	chr12:104152800-104156200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:104152800-104159000	Weak transcription	Fetal Muscle Trunk	muscle
42	chr12:104152800-104159200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr12:104152800-104159600	Weak transcription	Fetal Muscle Leg	muscle
44	chr12:104152800-104162800	Weak transcription	Brain Angular Gyrus	brain
45	chr12:104152800-104165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:104153000-104154200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:104153000-104154600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:104153000-104155800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:104153000-104156200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:104153200-104154600	Weak transcription	Fetal Stomach	stomach

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