Variant report

Variant	rs725281
Chromosome Location	chr22:29393195-29393196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29392383..29394290-chr22:29401537..29403639,2	MCF-7	breast:
2	chr22:29278862..29280383-chr22:29392380..29394372,2	K562	blood:

Variant related genes	Relation type
ENSG00000183579	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11912894	1.00[CEU][hapmap]
rs11913805	1.00[CEU][hapmap]
rs12169126	0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs12627758	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12628457	0.80[AMR][1000 genomes]
rs12628579	0.80[AMR][1000 genomes]
rs16987065	1.00[CEU][hapmap]
rs16987067	1.00[CEU][hapmap]
rs16987167	1.00[CEU][hapmap]
rs41382448	1.00[CEU][hapmap]
rs4508707	1.00[CEU][hapmap]
rs4823000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752839	0.92[JPT][hapmap]
rs5752842	0.93[JPT][hapmap]
rs5752851	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs5762891	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs5762893	1.00[JPT][hapmap]
rs5762900	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs5762906	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs5762907	0.93[JPT][hapmap]
rs5762919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs5762925	0.95[YRI][hapmap]
rs5762930	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs5762931	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs61697201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs722590	1.00[CEU][hapmap]
rs7288513	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7290364	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs8138320	1.00[CEU][hapmap]
rs8138963	1.00[CEU][hapmap]
rs8139248	1.00[CEU][hapmap]
rs8140511	1.00[CEU][hapmap]
rs8140640	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8140748	1.00[CEU][hapmap]
rs8141696	1.00[CEU][hapmap]
rs8141812	1.00[CEU][hapmap]
rs9306461	1.00[JPT][hapmap]
rs9625645	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs974370	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29365800-29394800	Weak transcription	Pancreas	Pancrea
2	chr22:29373600-29400200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr22:29374400-29395200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr22:29374600-29395600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr22:29374600-29400000	Weak transcription	Right Ventricle	heart
6	chr22:29374600-29401200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr22:29375800-29395400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:29379600-29400800	Weak transcription	Fetal Brain Female	brain
9	chr22:29380800-29400800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr22:29381000-29395600	Weak transcription	Esophagus	oesophagus
11	chr22:29381200-29400400	Weak transcription	Lung	lung
12	chr22:29381600-29395400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:29382000-29400200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr22:29382400-29393200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr22:29383400-29400200	Weak transcription	Right Atrium	heart
16	chr22:29383600-29400400	Weak transcription	Aorta	Aorta
17	chr22:29383800-29395400	Weak transcription	NHEK	skin
18	chr22:29383800-29399800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr22:29383800-29400000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr22:29384600-29395600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr22:29385000-29395200	Weak transcription	Left Ventricle	heart
22	chr22:29385000-29395600	Weak transcription	A549	lung
23	chr22:29385600-29394600	Weak transcription	Fetal Kidney	kidney
24	chr22:29385600-29395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr22:29385600-29400800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr22:29385600-29401000	Weak transcription	Colon Smooth Muscle	Colon
27	chr22:29385800-29397800	Weak transcription	Fetal Lung	lung
28	chr22:29386000-29395600	Weak transcription	Osteobl	bone
29	chr22:29386200-29395400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr22:29386200-29395600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr22:29386200-29400000	Weak transcription	Stomach Smooth Muscle	stomach
32	chr22:29386400-29395400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr22:29386400-29395800	Weak transcription	HMEC	breast
34	chr22:29386600-29395400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr22:29386800-29395600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr22:29387000-29395400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr22:29388600-29400400	Weak transcription	Placenta	Placenta
38	chr22:29388800-29399200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr22:29388800-29400200	Weak transcription	Brain Germinal Matrix	brain
40	chr22:29388800-29400800	Weak transcription	Gastric	stomach
41	chr22:29389000-29394800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr22:29389000-29395200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr22:29389000-29395600	Weak transcription	HSMM	muscle
44	chr22:29389000-29400000	Weak transcription	Brain Substantia Nigra	brain
45	chr22:29389200-29395400	Weak transcription	Ovary	ovary
46	chr22:29389200-29400000	Weak transcription	Brain Hippocampus Middle	brain
47	chr22:29389400-29394800	Weak transcription	Brain Anterior Caudate	brain
48	chr22:29389400-29395600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:29389400-29399800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr22:29389400-29400000	Weak transcription	Liver	Liver

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