Variant report

Variant	rs5762900
Chromosome Location	chr22:29327907-29327908
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29326669..29328681-chr22:29332025..29335341,3	MCF-7	breast:
2	chr22:29325211..29329451-chr22:29330662..29333324,4	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12627758	1.00[JPT][hapmap]
rs16986814	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16986873	0.90[EUR][1000 genomes]
rs2206061	1.00[MEX][hapmap]
rs2881637	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4823000	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs5752830	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5752839	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752842	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752851	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs5762873	0.89[ASN][1000 genomes]
rs5762876	0.89[ASN][1000 genomes]
rs5762890	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762893	0.86[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5762895	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762906	0.85[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762907	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762919	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs5997401	0.89[MEX][hapmap]
rs6005861	0.88[MEX][hapmap]
rs725281	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7286026	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7288513	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7290364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73388860	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8137589	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8140640	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs9306461	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625575	1.00[MEX][hapmap]
rs9625613	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625621	0.90[EUR][1000 genomes]
rs9625622	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625628	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625640	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9625641	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625645	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9625647	1.00[ASN][1000 genomes]
rs9625657	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs974370	0.92[JPT][hapmap]

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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29314400-29342800	Weak transcription	Brain Substantia Nigra	brain
2	chr22:29314800-29328400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:29317800-29329400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr22:29320400-29328800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr22:29320600-29330800	Weak transcription	Fetal Muscle Leg	muscle
6	chr22:29320600-29332200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr22:29321000-29339600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr22:29322000-29336600	Weak transcription	NHEK	skin
9	chr22:29322200-29333400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:29322400-29329600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr22:29323600-29329400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr22:29324000-29335400	Weak transcription	Colon Smooth Muscle	Colon
13	chr22:29324800-29329000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr22:29325200-29328600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:29325200-29328800	Enhancers	Gastric	stomach
16	chr22:29325200-29330000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr22:29325200-29330200	Enhancers	Fetal Kidney	kidney
18	chr22:29325400-29331200	Enhancers	Liver	Liver
19	chr22:29325600-29328400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr22:29325600-29331200	Weak transcription	Brain Hippocampus Middle	brain
21	chr22:29325600-29331600	Enhancers	Fetal Intestine Small	intestine
22	chr22:29325800-29328400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr22:29325800-29329400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:29325800-29334200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr22:29326200-29328600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr22:29326200-29330200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr22:29326200-29331600	Enhancers	Duodenum Mucosa	Duodenum
28	chr22:29326400-29328200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr22:29326400-29328200	Enhancers	Psoas Muscle	Psoas
30	chr22:29326400-29328200	Enhancers	Small Intestine	intestine
31	chr22:29326400-29328600	Enhancers	Aorta	Aorta
32	chr22:29326400-29328600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr22:29326400-29328600	Enhancers	Right Atrium	heart
34	chr22:29326400-29328600	Enhancers	Stomach Mucosa	stomach
35	chr22:29326400-29328800	Enhancers	Pancreas	Pancrea
36	chr22:29326400-29329600	Enhancers	Brain Anterior Caudate	brain
37	chr22:29326400-29331800	Enhancers	Fetal Intestine Large	intestine
38	chr22:29326600-29328800	Enhancers	Brain Angular Gyrus	brain
39	chr22:29326600-29336000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr22:29326800-29328600	Weak transcription	A549	lung
41	chr22:29326800-29328800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr22:29326800-29329400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr22:29326800-29329400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr22:29326800-29329800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr22:29327000-29328000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr22:29327000-29328000	Weak transcription	Left Ventricle	heart
47	chr22:29327000-29328000	Weak transcription	Ovary	ovary
48	chr22:29327000-29328000	Weak transcription	Right Ventricle	heart
49	chr22:29327000-29328600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr22:29327000-29328800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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