Variant report

Variant	rs5752801
Chromosome Location	chr22:29201217-29201218
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	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183765	Chromatin interaction
ENSG00000100209	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12628211	0.83[ASN][1000 genomes]
rs2097461	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2239815	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2269577	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2347447	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2881635	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35259224	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3788409	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752795	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752798	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752804	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752807	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752809	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752812	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752813	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762784	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762788	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5762795	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762803	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs5762815	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762824	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762825	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5762854	0.84[EUR][1000 genomes]
rs5997408	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6005867	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6005869	0.82[AMR][1000 genomes]
rs6005872	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6005881	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6005892	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6005916	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7287124	0.83[ASN][1000 genomes]
rs7287806	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs763073	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8137969	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625566	0.81[ASN][1000 genomes]
rs9625588	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][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	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	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
3	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5752801	CCDC117	Cis_1M	lymphoblastoid	RTeQTL
rs5752801	XBP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197000-29205400	Weak transcription	Spleen	Spleen
2	chr22:29197200-29202600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:29197200-29204000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr22:29197200-29208200	Weak transcription	Esophagus	oesophagus
5	chr22:29197200-29209800	Weak transcription	Left Ventricle	heart
6	chr22:29197200-29214200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr22:29197400-29214400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:29197600-29209800	Weak transcription	Ovary	ovary
11	chr22:29197800-29204000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr22:29197800-29214200	Weak transcription	Right Ventricle	heart
13	chr22:29198000-29203800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr22:29198000-29225200	Weak transcription	HSMM	muscle
15	chr22:29198200-29203600	Weak transcription	Pancreas	Pancrea
16	chr22:29198200-29204600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
18	chr22:29198400-29204600	Weak transcription	Brain Hippocampus Middle	brain
19	chr22:29198400-29206200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr22:29198400-29208200	Weak transcription	Fetal Lung	lung
21	chr22:29198400-29208400	Weak transcription	Lung	lung
22	chr22:29198400-29209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr22:29198400-29214000	Weak transcription	Colonic Mucosa	Colon
24	chr22:29198400-29214400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:29198400-29215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr22:29198600-29203800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:29198600-29203800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr22:29198600-29204000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr22:29198600-29204600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr22:29198600-29206800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr22:29198600-29207200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr22:29198600-29207200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr22:29198600-29210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr22:29198600-29211200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr22:29198600-29212600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr22:29198600-29214200	Weak transcription	Colon Smooth Muscle	Colon
38	chr22:29198600-29214400	Weak transcription	Aorta	Aorta
39	chr22:29198600-29214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr22:29198600-29219400	Weak transcription	NHLF	lung
41	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr22:29198600-29225200	Weak transcription	Osteobl	bone
43	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
44	chr22:29198800-29203800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr22:29198800-29203800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr22:29198800-29203800	Weak transcription	Fetal Intestine Large	intestine
47	chr22:29198800-29203800	Weak transcription	Fetal Muscle Leg	muscle
48	chr22:29198800-29204600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr22:29198800-29204600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:29198800-29204600	Weak transcription	Adipose Nuclei	Adipose

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