Variant report

Variant	rs5752804
Chromosome Location	chr22:29207492-29207493
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr22:29206766-29207567	HepG2	liver:	n/a	n/a
2	PAX5	chr22:29207060-29207541	GM12878	blood:	n/a	n/a
3	POLR2A	chr22:29207101-29207546	HepG2	liver:	n/a	n/a
4	POLR2A	chr22:29206705-29208122	HL-60	blood:	n/a	n/a
5	FOXA1	chr22:29206756-29207492	HepG2	liver:	n/a	n/a
6	EP300	chr22:29206676-29207533	HepG2	liver:	n/a	n/a
7	POLR2A	chr22:29206564-29207536	HL-60	blood:	n/a	n/a
8	SP1	chr22:29206700-29207509	HepG2	liver:	n/a	n/a
9	HDAC2	chr22:29206785-29207599	HepG2	liver:	n/a	chr22:29207149-29207163
10	NFIC	chr22:29206994-29207608	HepG2	liver:	n/a	n/a
11	MYBL2	chr22:29206627-29207540	HepG2	liver:	n/a	n/a
12	FOXA1	chr22:29206756-29207507	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29195974..29199914-chr22:29206456..29209636,5	K562	blood:
2	chr22:29205328..29207798-chr6:30697845..30700458,2	MCF-7	breast:
3	chr17:57918590..57921069-chr22:29206794..29208506,2	MCF-7	breast:
4	chr17:57916592..57918397-chr22:29207253..29209667,2	MCF-7	breast:
5	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
6	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000272858	TF binding region
ENSG00000100209	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12628211	0.94[ASN][1000 genomes]
rs2097461	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239815	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2269577	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2347447	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2881635	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35259224	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788409	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752795	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752798	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5752801	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5752807	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752809	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752812	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752813	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762784	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762788	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5762795	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5762803	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5762815	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5762824	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762825	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762853	0.83[ASN][1000 genomes]
rs5762854	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5762863	0.83[ASN][1000 genomes]
rs5762864	0.83[ASN][1000 genomes]
rs5762865	0.81[EUR][1000 genomes]
rs5762867	0.80[ASN][1000 genomes]
rs5997408	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005867	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005869	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6005872	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005881	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005892	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6005916	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005927	0.83[ASN][1000 genomes]
rs6005929	0.82[ASN][1000 genomes]
rs7287124	0.94[ASN][1000 genomes]
rs7287806	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs763073	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8137969	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9625566	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9625588	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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
rs5752804	XBP1	Cis_1M	lymphoblastoid	RTeQTL
rs5752804	CCDC117	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29197200-29208200	Weak transcription	Esophagus	oesophagus
2	chr22:29197200-29209800	Weak transcription	Left Ventricle	heart
3	chr22:29197200-29214200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr22:29197200-29231600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr22:29197400-29214400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr22:29197400-29220400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr22:29197600-29209800	Weak transcription	Ovary	ovary
8	chr22:29197800-29214200	Weak transcription	Right Ventricle	heart
9	chr22:29198000-29225200	Weak transcription	HSMM	muscle
10	chr22:29198200-29218600	Weak transcription	Brain Angular Gyrus	brain
11	chr22:29198400-29208200	Weak transcription	Fetal Lung	lung
12	chr22:29198400-29208400	Weak transcription	Lung	lung
13	chr22:29198400-29209800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:29198400-29214000	Weak transcription	Colonic Mucosa	Colon
15	chr22:29198400-29214400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29198400-29215600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr22:29198400-29225200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr22:29198600-29210600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr22:29198600-29211200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:29198600-29212600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr22:29198600-29214200	Weak transcription	Colon Smooth Muscle	Colon
22	chr22:29198600-29214400	Weak transcription	Aorta	Aorta
23	chr22:29198600-29214600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr22:29198600-29219400	Weak transcription	NHLF	lung
25	chr22:29198600-29225200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr22:29198600-29225200	Weak transcription	Osteobl	bone
27	chr22:29198600-29231400	Weak transcription	HSMMtube	muscle
28	chr22:29198800-29207800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr22:29198800-29214200	Weak transcription	Stomach Smooth Muscle	stomach
30	chr22:29198800-29214400	Weak transcription	Fetal Heart	heart
31	chr22:29198800-29230800	Weak transcription	NHEK	skin
32	chr22:29199000-29208400	Weak transcription	NHDF-Ad	bronchial
33	chr22:29200600-29231400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr22:29200800-29208200	Weak transcription	Fetal Stomach	stomach
35	chr22:29203800-29208200	Enhancers	Liver	Liver
36	chr22:29204800-29214600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:29205000-29214200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr22:29205200-29214400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr22:29205200-29218800	Weak transcription	Brain Hippocampus Middle	brain
40	chr22:29205400-29209000	Weak transcription	A549	lung
41	chr22:29205400-29217000	Weak transcription	Gastric	stomach
42	chr22:29205400-29225600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr22:29206200-29207800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr22:29206200-29208000	Flanking Active TSS	Fetal Thymus	thymus
45	chr22:29206200-29208400	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr22:29206200-29208400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr22:29206200-29208600	Enhancers	Primary B cells from peripheral blood	blood
48	chr22:29206200-29215600	Enhancers	Stomach Mucosa	stomach
49	chr22:29206400-29208200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr22:29206400-29208200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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