Variant report

Variant	rs3825258
Chromosome Location	chr12:12279395-12279396
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1015830	0.93[ASN][1000 genomes]
rs10743981	0.81[EUR][1000 genomes]
rs1074992	0.94[CEU][hapmap]
rs10845498	1.00[CEU][hapmap]
rs10845504	0.94[CEU][hapmap]
rs11054697	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054752	0.81[EUR][1000 genomes]
rs12580417	0.84[EUR][1000 genomes]
rs16907786	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16907810	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2075241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160521	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2160589	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs2300231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4265667	0.83[EUR][1000 genomes]
rs4763789	0.82[EUR][1000 genomes]
rs7134001	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7313285	0.83[EUR][1000 genomes]
rs7968660	0.94[CEU][hapmap]

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	chr12:12261600-12301400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr12:12261800-12288000	Weak transcription	Gastric	stomach
3	chr12:12262400-12335600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:12262800-12284800	Weak transcription	Aorta	Aorta
5	chr12:12263800-12314600	Weak transcription	Esophagus	oesophagus
6	chr12:12264000-12301400	Weak transcription	Right Ventricle	heart
7	chr12:12264200-12284600	Weak transcription	Pancreas	Pancrea
8	chr12:12264400-12284800	Weak transcription	Lung	lung
9	chr12:12264400-12311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:12265600-12303400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:12267800-12282400	Weak transcription	Fetal Intestine Small	intestine
12	chr12:12267800-12301600	Weak transcription	NHLF	lung
13	chr12:12268800-12301600	Weak transcription	Brain Substantia Nigra	brain
14	chr12:12269200-12279600	Weak transcription	Fetal Brain Male	brain
15	chr12:12269600-12343200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:12270600-12284800	Weak transcription	Spleen	Spleen
17	chr12:12271000-12284400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:12271000-12301600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr12:12271200-12280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:12271400-12281200	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:12271400-12286600	Strong transcription	Liver	Liver
22	chr12:12271400-12306600	Weak transcription	Small Intestine	intestine
23	chr12:12271600-12288400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:12271600-12294200	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:12271800-12279800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:12271800-12285000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:12271800-12285600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:12271800-12286400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:12272000-12285000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:12272000-12286000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr12:12272200-12344600	Weak transcription	Primary B cells from cord blood	blood
32	chr12:12272400-12325200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr12:12272600-12280800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr12:12272600-12285000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:12272600-12288400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr12:12272600-12305000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr12:12273000-12279800	Strong transcription	Fetal Thymus	thymus
38	chr12:12273000-12283600	Strong transcription	Fetal Muscle Leg	muscle
39	chr12:12273200-12279800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:12273200-12279800	Strong transcription	Fetal Intestine Large	intestine
41	chr12:12273400-12280000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:12273400-12283400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:12273400-12286600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:12273600-12301600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr12:12274200-12287800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:12274400-12284600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:12274600-12313600	Weak transcription	Colonic Mucosa	Colon
48	chr12:12275000-12281000	Strong transcription	A549	lung
49	chr12:12275000-12303400	Weak transcription	GM12878-XiMat	blood
50	chr12:12275200-12280000	Strong transcription	Rectal Mucosa Donor 31	rectum

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