Variant report

Variant	rs12428617
Chromosome Location	chr13:76373826-76373827
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12428250	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12428746	1.00[CEU][hapmap];0.87[AFR][1000 genomes]
rs12429534	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12430034	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1542115	0.87[AFR][1000 genomes]
rs17065053	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17065074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17065145	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs1924094	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2120060	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2120061	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2241913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3759445	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3783025	0.81[ASN][1000 genomes]
rs3825439	0.80[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs41287008	0.81[ASN][1000 genomes]
rs4885357	1.00[CEU][hapmap];0.87[AFR][1000 genomes]
rs56030259	0.87[EUR][1000 genomes]
rs61958154	0.94[EUR][1000 genomes]
rs61958155	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61958156	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61958157	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61959560	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61959561	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61959635	0.87[AFR][1000 genomes]
rs629443	0.84[ASN][1000 genomes]
rs9530471	0.80[CHB][hapmap];0.93[JPT][hapmap]
rs9544047	0.90[ASN][1000 genomes]
rs9544050	0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs9544051	0.80[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs9544053	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr13:76361800-76377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:76362000-76376600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr13:76362600-76377000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:76363000-76377000	Weak transcription	GM12878-XiMat	blood
6	chr13:76363200-76376400	Weak transcription	Esophagus	oesophagus
7	chr13:76363200-76381800	Weak transcription	Fetal Stomach	stomach
8	chr13:76364600-76385000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:76366400-76376600	Weak transcription	Left Ventricle	heart
10	chr13:76366400-76380200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:76366800-76374800	Weak transcription	Aorta	Aorta
12	chr13:76366800-76376600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr13:76366800-76379400	Weak transcription	Pancreas	Pancrea
14	chr13:76366800-76379400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr13:76366800-76380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr13:76366800-76380200	Weak transcription	Lung	lung
17	chr13:76367000-76374000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr13:76367000-76377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr13:76367000-76379800	Weak transcription	Brain Angular Gyrus	brain
20	chr13:76367000-76380200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr13:76367000-76387000	Weak transcription	Ovary	ovary
22	chr13:76367200-76374200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:76367200-76377400	Weak transcription	Fetal Kidney	kidney
24	chr13:76367400-76374000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr13:76367400-76374400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr13:76367400-76377400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr13:76367400-76380600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr13:76367400-76384400	Weak transcription	Fetal Lung	lung
29	chr13:76369000-76374000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:76369600-76377400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:76369800-76376800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
33	chr13:76370800-76375200	Genic enhancers	NHDF-Ad	bronchial
34	chr13:76370800-76375800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:76370800-76378800	Genic enhancers	Osteobl	bone
36	chr13:76370800-76382400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr13:76371000-76375400	Genic enhancers	HSMM	muscle
38	chr13:76371400-76376600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr13:76371400-76376600	Weak transcription	Brain Anterior Caudate	brain
40	chr13:76371400-76379000	Weak transcription	Placenta	Placenta
41	chr13:76371600-76374400	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr13:76371600-76375400	Genic enhancers	NHLF	lung
43	chr13:76371600-76376400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:76371600-76377000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:76371600-76377200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr13:76371800-76375000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr13:76371800-76375600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr13:76371800-76376600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr13:76371800-76377200	Enhancers	Fetal Heart	heart
50	chr13:76372000-76375000	Enhancers	A549	lung

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