Variant report

Variant	rs12424361
Chromosome Location	chr12:12278687-12278688
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:12276861..12279335-chr12:12282362..12284399,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10082834	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466847	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466848	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772531	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10845497	1.00[ASN][1000 genomes]
rs10845500	1.00[ASN][1000 genomes]
rs11054695	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054696	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054702	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054705	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054706	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054707	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054709	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054710	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054713	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054746	1.00[ASN][1000 genomes]
rs11054767	1.00[ASN][1000 genomes]
rs1123213	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11829211	1.00[ASN][1000 genomes]
rs11831610	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12296239	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306293	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306537	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307111	1.00[ASN][1000 genomes]
rs12309246	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12309338	1.00[ASN][1000 genomes]
rs12309495	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12310020	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311202	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311922	1.00[ASN][1000 genomes]
rs12316043	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12422890	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424332	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425185	1.00[ASN][1000 genomes]
rs12425699	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13377971	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907789	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448423	1.00[ASN][1000 genomes]
rs56259928	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58682800	1.00[ASN][1000 genomes]
rs59386755	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311064	1.00[ASN][1000 genomes]
rs7979919	1.00[ASN][1000 genomes]
rs9630249	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630250	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630266	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv529005	chr12:12254756-12412795	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	esv3427115	chr12:12262415-12432411	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
4	nsv898806	chr12:12264471-12453808	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr12:12261600-12301400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr12:12261800-12288000	Weak transcription	Gastric	stomach
4	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:12262800-12284800	Weak transcription	Aorta	Aorta
6	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
7	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
8	chr12:12264200-12284600	Weak transcription	Pancreas	Pancrea
9	chr12:12264400-12284800	Weak transcription	Lung	lung
10	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:12265400-12279000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:12267800-12282400	Weak transcription	Fetal Intestine Small	intestine
14	chr12:12267800-12301600	Weak transcription	NHLF	lung
15	chr12:12268400-12279000	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:12268800-12301600	Weak transcription	Brain Substantia Nigra	brain
17	chr12:12269200-12279600	Weak transcription	Fetal Brain Male	brain
18	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:12270600-12284800	Weak transcription	Spleen	Spleen
20	chr12:12271000-12284400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:12271000-12301600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:12271200-12280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr12:12271400-12281200	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:12271400-12286600	Strong transcription	Liver	Liver
25	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
26	chr12:12271600-12288400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:12271600-12294200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:12271800-12279800	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:12271800-12285000	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:12271800-12285600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr12:12271800-12286400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:12272000-12285000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr12:12272000-12286000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
35	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:12272600-12280800	Strong transcription	Duodenum Mucosa	Duodenum
37	chr12:12272600-12285000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:12272600-12288400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr12:12273000-12278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:12273000-12279800	Strong transcription	Fetal Thymus	thymus
42	chr12:12273000-12283600	Strong transcription	Fetal Muscle Leg	muscle
43	chr12:12273200-12279800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:12273200-12279800	Strong transcription	Fetal Intestine Large	intestine
45	chr12:12273400-12280000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr12:12273400-12283400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:12273400-12286600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr12:12273600-12301600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr12:12274200-12287800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:12274400-12279200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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