Variant report

Variant	rs12229599
Chromosome Location	chr12:104154375-104154376
allele	C/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: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1057892	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12422418	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12422615	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12422701	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12423912	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12423929	0.94[AMR][1000 genomes]
rs12423994	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12424929	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12424984	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12425283	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12425537	0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12426526	0.92[AMR][1000 genomes]
rs17034464	0.94[AMR][1000 genomes]
rs17034593	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17794246	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2289258	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3751196	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55724382	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55810720	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55932227	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55987022	0.83[AMR][1000 genomes]
rs56255894	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61748068	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

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

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104140600-104154600	Weak transcription	Aorta	Aorta
2	chr12:104142800-104154600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:104142800-104154600	Weak transcription	NHEK	skin
4	chr12:104145600-104154800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:104145800-104166800	Weak transcription	Right Atrium	heart
6	chr12:104146000-104154600	Weak transcription	HSMM	muscle
7	chr12:104146200-104169400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:104147000-104159600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:104147000-104165400	Strong transcription	Stomach Smooth Muscle	stomach
10	chr12:104147400-104155800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:104148200-104154400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:104149000-104156800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:104150000-104156600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr12:104150000-104166800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:104150600-104155200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:104151400-104154800	Weak transcription	NH-A	brain
17	chr12:104151400-104158000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:104151600-104155000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:104151600-104170400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr12:104151800-104154800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:104152000-104159800	Weak transcription	Lung	lung
22	chr12:104152400-104154800	Weak transcription	HSMMtube	muscle
23	chr12:104152400-104159400	Weak transcription	Gastric	stomach
24	chr12:104152400-104160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:104152400-104162600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:104152400-104162800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:104152600-104154400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:104152600-104158600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr12:104152600-104160600	Strong transcription	Spleen	Spleen
30	chr12:104152600-104161600	Strong transcription	HMEC	breast
31	chr12:104152600-104162600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:104152600-104162600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr12:104152600-104162800	Weak transcription	Psoas Muscle	Psoas
34	chr12:104152600-104171200	Weak transcription	Esophagus	oesophagus
35	chr12:104152800-104156200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:104152800-104159000	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:104152800-104159200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:104152800-104159600	Weak transcription	Fetal Muscle Leg	muscle
39	chr12:104152800-104162800	Weak transcription	Brain Angular Gyrus	brain
40	chr12:104152800-104165400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:104153000-104154600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:104153000-104155800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:104153000-104156200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:104153200-104154600	Weak transcription	Fetal Stomach	stomach
45	chr12:104153200-104162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:104153400-104156000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:104153800-104155400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr12:104153800-104161600	Strong transcription	Liver	Liver
50	chr12:104154200-104155400	Strong transcription	A549	lung

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