Variant report

Variant	rs17882867
Chromosome Location	chr22:29132364-29132365
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU5F1	chr22:29132241-29132713	H1-hESC	embryonic stem cell:	n/a	chr22:29132479-29132493 chr22:29132479-29132493 chr22:29132480-29132494 chr22:29132479-29132493 chr22:29132321-29132329
2	NANOG	chr22:29132352-29132581	H1-hESC	embryonic stem cell:	n/a	chr22:29132477-29132491
3	TCF12	chr22:29132169-29132601	H1-hESC	embryonic stem cell:	n/a	n/a
4	NANOG	chr22:29132310-29132577	H1-hESC	embryonic stem cell:	n/a	chr22:29132477-29132491

No.	Distal block	Cell Line	Cell type
1	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:
2	chr22:29129415..29131675-chr22:29131863..29134375,2	MCF-7	breast:
3	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:
4	chr22:29131911..29134961-chr22:29136110..29138842,3	K562	blood:

Variant related genes	Relation type
CHEK2	TF binding region
ENSG00000272858	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs16986630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16986646	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16986711	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs16986719	0.84[ASN][1000 genomes]
rs16986739	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs17879919	1.00[AMR][1000 genomes]
rs17883328	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17885975	1.00[AMR][1000 genomes]
rs17885996	1.00[AMR][1000 genomes]
rs1805129	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2180459	1.00[JPT][hapmap]
rs5762681	1.00[JPT][hapmap]
rs59025667	0.84[ASN][1000 genomes]
rs6005807	1.00[JPT][hapmap]
rs6005844	0.86[EUR][1000 genomes]
rs6005846	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6005851	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60740682	0.82[ASN][1000 genomes]
rs9625587	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	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
4	nsv513775	chr22:29083731-29137822	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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
6	nsv517951	chr22:29105558-29135889	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
2	chr22:29082800-29137600	Weak transcription	Spleen	Spleen
3	chr22:29090600-29137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29090600-29137200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr22:29100400-29137200	Weak transcription	Pancreas	Pancrea
6	chr22:29105600-29137200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr22:29107600-29136800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr22:29108400-29137200	Weak transcription	Right Atrium	heart
9	chr22:29109000-29137000	Weak transcription	HMEC	breast
10	chr22:29109000-29137200	Weak transcription	Liver	Liver
11	chr22:29109000-29137200	Weak transcription	HSMM	muscle
12	chr22:29111200-29136600	Weak transcription	HUVEC	blood vessel
13	chr22:29112000-29137600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr22:29117200-29136800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr22:29117200-29137200	Weak transcription	NHLF	lung
16	chr22:29118000-29137600	Weak transcription	Ovary	ovary
17	chr22:29118200-29137200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr22:29119400-29137200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr22:29119800-29137200	Weak transcription	A549	lung
20	chr22:29120000-29137200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr22:29121200-29137400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr22:29121400-29137200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:29121600-29136600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr22:29121800-29137200	Weak transcription	Placenta	Placenta
25	chr22:29123400-29137200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr22:29124400-29133800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr22:29125000-29137200	Weak transcription	NHDF-Ad	bronchial
28	chr22:29125400-29137200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr22:29125600-29137200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr22:29126000-29134600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:29126200-29136600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr22:29126800-29137400	Weak transcription	Gastric	stomach
33	chr22:29127400-29137400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr22:29127600-29132600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr22:29129200-29136200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr22:29129600-29136800	Weak transcription	Primary B cells from cord blood	blood
37	chr22:29129600-29137200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr22:29130200-29137200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr22:29130400-29134000	Weak transcription	Hela-S3	cervix
40	chr22:29130400-29136600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr22:29130400-29137200	Weak transcription	Fetal Muscle Leg	muscle
42	chr22:29130600-29133800	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr22:29130600-29134200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr22:29130600-29134800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr22:29130600-29135600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:29130600-29135800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr22:29130600-29135800	Weak transcription	Fetal Lung	lung
48	chr22:29130600-29136200	Weak transcription	GM12878-XiMat	blood
49	chr22:29130600-29136800	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr22:29130600-29136800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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