Variant report

Variant	rs17880459
Chromosome Location	chr22:29137357-29137358
allele	C/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	ZNF384	chr22:29137259-29137889	K562	blood:	n/a	n/a
2	POLR2A	chr22:29137326-29139085	GM12891	blood:	n/a	n/a
3	RUNX3	chr22:29137335-29138728	GM12878	blood:	n/a	n/a
4	MAZ	chr22:29137352-29139079	IMR90	lung:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
5	POLR2A	chr22:29137312-29138705	GM12892	blood:	n/a	n/a
6	SP1	chr22:29137297-29138968	HCT-116	colon:	n/a	chr22:29137979-29137991 chr22:29138429-29138438 chr22:29137981-29137990 chr22:29137999-29138020 chr22:29138428-29138440 chr22:29137979-29137991 chr22:29137855-29137864 chr22:29138491-29138500 chr22:29137870-29137891 chr22:29138428-29138440
7	MXI1	chr22:29137076-29139717	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr22:29137259-29137360	H1-hESC	embryonic stem cell:	n/a	n/a
9	MYC	chr22:29137301-29138626	K562	blood:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
10	RFX5	chr22:29137339-29138017	K562	blood:	n/a	chr22:29138001-29138010 chr22:29137842-29137851
11	JUND	chr22:29137241-29138652	K562	blood:	n/a	chr22:29138427-29138436 chr22:29137748-29137755 chr22:29137748-29137757 chr22:29137843-29137852 chr22:29137492-29137502 chr22:29137746-29137757 chr22:29138002-29138011 chr22:29137751-29137759
12	POLR2A	chr22:29137310-29139038	Hela-S3	cervix:	n/a	n/a
13	HCFC1	chr22:29137292-29138934	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr22:29137260-29138916	K562	blood:	n/a	n/a
15	POLR2A	chr22:29137347-29138823	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr22:29137351-29138547	GM12892	blood:	n/a	n/a
17	TBP	chr22:29137304-29138638	K562	blood:	n/a	n/a
18	E2F4	chr22:29137256-29138801	MCF10A-Er-Src	breast:	n/a	chr22:29138000-29138009 chr22:29137862-29137872 chr22:29137841-29137850
19	MAX	chr22:29137341-29138786	ECC-1	luminal epithelium:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
20	TAF1	chr22:29137353-29138745	GM12878	blood:	n/a	n/a
21	POLR2A	chr22:29137341-29138790	GM12878	blood:	n/a	n/a
22	GTF3C2	chr22:29137263-29137896	Hela-S3	cervix:	n/a	n/a
23	FOSL2	chr22:29137328-29138426	A549	lung:	n/a	chr22:29137747-29137758 chr22:29137748-29137755 chr22:29137748-29137757 chr22:29137843-29137852 chr22:29137492-29137502 chr22:29138002-29138011 chr22:29137751-29137759
24	FOS	chr22:29137347-29138134	MCF10A-Er-Src	breast:	n/a	chr22:29137748-29137755 chr22:29137748-29137757 chr22:29137843-29137852 chr22:29137492-29137502 chr22:29137746-29137757 chr22:29138002-29138011 chr22:29137751-29137759
25	MTA3	chr22:29137194-29139109	GM12878	blood:	n/a	n/a
26	SIN3AK20	chr22:29137327-29139028	MCF-7	breast:	n/a	n/a
27	MYC	chr22:29137338-29138644	K562	blood:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
28	GTF3C2	chr22:29137283-29138491	K562	blood:	n/a	n/a
29	RFX5	chr22:29137341-29138725	Hela-S3	cervix:	n/a	chr22:29138001-29138010 chr22:29137842-29137851
30	POLR2A	chr22:29137345-29138924	Hela-S3	cervix:	n/a	n/a
31	EP300	chr22:29137280-29138596	GM12878	blood:	n/a	chr22:29137613-29137627 chr22:29137789-29137805 chr22:29137632-29137645 chr22:29137945-29137959 chr22:29137748-29137757
32	PML	chr22:29137306-29138545	K562	blood:	n/a	chr22:29137421-29137429 chr22:29138409-29138417
33	POLR2A	chr22:29137263-29139028	MCF-7	breast:	n/a	n/a
34	TBL1XR1	chr22:29137357-29138559	K562	blood:	n/a	n/a
35	TAL1	chr22:29137326-29138177	K562	blood:	n/a	n/a
36	POLR2A	chr22:29137353-29138800	Raji	blood:	n/a	n/a
37	POLR2A	chr22:29137151-29138872	SK-N-MC	brain:	n/a	n/a
38	TCF12	chr22:29137280-29138737	A549	lung:	n/a	n/a
39	PML	chr22:29137217-29138937	GM12878	blood:	n/a	chr22:29137421-29137429 chr22:29138409-29138417
40	HEY1	chr22:29137346-29138185	K562	blood:	n/a	chr22:29137857-29137872
41	SPI1	chr22:29137326-29138221	HL-60	blood:	n/a	chr22:29137736-29137749 chr22:29137738-29137747
42	REST	chr22:29137348-29138322	HL-60	blood:	n/a	n/a
43	NFIC	chr22:29137270-29138557	GM12878	blood:	n/a	n/a
44	POLR2A	chr22:29137356-29138850	PFSK-1	brain:	n/a	n/a
45	GABPA	chr22:29137328-29138919	MCF-7	breast:	n/a	n/a
46	SPI1	chr22:29137247-29138353	GM12878	blood:	n/a	chr22:29137736-29137749 chr22:29137738-29137747
47	MAX	chr22:29137354-29138832	GM12878	blood:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
48	POLR2A	chr22:29137276-29138564	K562	blood:	n/a	n/a
49	POLR2A	chr22:29137284-29138699	H1-hESC	embryonic stem cell:	n/a	n/a
50	JUN	chr22:29137221-29138709	K562	blood:	n/a	chr22:29138427-29138436 chr22:29137748-29137755 chr22:29137748-29137757 chr22:29137843-29137852 chr22:29137492-29137502 chr22:29138002-29138011 chr22:29137751-29137759

No.	Distal block	Cell Line	Cell type
1	chr22:29126583..29142031-chr22:29203252..29220632,67	MCF-7	breast:
2	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:
3	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
4	chr22:29137011..29139217-chr22:29662922..29665353,2	MCF-7	breast:
5	chr22:29133133..29134961-chr22:29136110..29137715,2	K562	blood:
6	chr22:29136431..29140671-chr22:29167494..29170117,5	K562	blood:
7	chr22:29134319..29139472-chr22:29186598..29194420,8	K562	blood:
8	chr14:24681489..24683896-chr22:29136971..29139325,2	MCF-7	breast:
9	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
10	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
11	chr22:29134224..29141746-chr22:29191206..29200044,27	MCF-7	breast:
12	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:
13	chr22:29124921..29127441-chr22:29136398..29138709,2	K562	blood:

Variant related genes	Relation type
HSCB	TF binding region
ENSG00000183765	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000272858	Chromatin interaction
ENSG00000100219	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000182944	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000159873	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17879734	0.80[AFR][1000 genomes]
rs17880353	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17881056	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17882607	0.82[AFR][1000 genomes]
rs17883144	0.80[AFR][1000 genomes]
rs17884212	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs17885109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17885728	0.80[AFR][1000 genomes]
rs17885892	0.82[AFR][1000 genomes]
rs35255776	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3788408	0.82[AFR][1000 genomes]
rs5762814	1.00[YRI][hapmap]
rs8138111	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9620817	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17880459	CHEK2	cis	lymphoblastoid	seeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

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	chr22:29112000-29137600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr22:29118000-29137600	Weak transcription	Ovary	ovary
5	chr22:29121200-29137400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr22:29126800-29137400	Weak transcription	Gastric	stomach
7	chr22:29127400-29137400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr22:29130600-29137400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr22:29130600-29137400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr22:29136000-29139400	Active TSS	K562	blood
11	chr22:29136200-29137400	Flanking Active TSS	Dnd41	blood
12	chr22:29136400-29137400	Enhancers	Fetal Lung	lung
13	chr22:29136400-29139200	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr22:29136600-29137400	Enhancers	Primary B cells from peripheral blood	blood
15	chr22:29136600-29139600	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr22:29136800-29137400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr22:29136800-29137400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr22:29136800-29138800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr22:29136800-29138800	Active TSS	GM12878-XiMat	blood
20	chr22:29136800-29138800	Active TSS	Hela-S3	cervix
21	chr22:29137000-29137400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr22:29137000-29138000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr22:29137000-29138800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr22:29137000-29138800	Active TSS	HMEC	breast
25	chr22:29137000-29139400	Active TSS	H9 Cell Line	embryonic stem cell
26	chr22:29137000-29139400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr22:29137200-29137400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr22:29137200-29137400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr22:29137200-29137400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr22:29137200-29137400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr22:29137200-29137400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr22:29137200-29137400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr22:29137200-29137400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr22:29137200-29137400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr22:29137200-29137400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr22:29137200-29137400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr22:29137200-29137400	Enhancers	Adipose Nuclei	Adipose
38	chr22:29137200-29137400	Active TSS	Brain Angular Gyrus	brain
39	chr22:29137200-29137400	Active TSS	Brain Hippocampus Middle	brain
40	chr22:29137200-29137400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr22:29137200-29137400	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr22:29137200-29137400	Flanking Active TSS	Fetal Intestine Small	intestine
43	chr22:29137200-29137400	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr22:29137200-29137400	Enhancers	Placenta	Placenta
45	chr22:29137200-29137400	Flanking Active TSS	Fetal Stomach	stomach
46	chr22:29137200-29137400	Enhancers	Pancreas	Pancrea
47	chr22:29137200-29137400	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr22:29137200-29137400	Enhancers	Right Atrium	heart
49	chr22:29137200-29137400	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr22:29137200-29137400	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links