Variant report

Variant	rs17879734
Chromosome Location	chr22:29137471-29137472
allele	A/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	ARID3A	chr22:29137362-29138120	K562	blood:	n/a	n/a
4	RUNX3	chr22:29137335-29138728	GM12878	blood:	n/a	n/a
5	HEY1	chr22:29137448-29138895	HepG2	liver:	n/a	chr22:29137857-29137872
6	MAZ	chr22:29137352-29139079	IMR90	lung:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
7	POLR2A	chr22:29137312-29138705	GM12892	blood:	n/a	n/a
8	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
9	GABPA	chr22:29137434-29138921	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr22:29137455-29138236	K562	blood:	n/a	n/a
11	FOXM1	chr22:29137449-29138723	GM12878	blood:	n/a	n/a
12	ZMIZ1	chr22:29137440-29138336	K562	blood:	n/a	n/a
13	MXI1	chr22:29137076-29139717	SK-N-SH	brain:	n/a	n/a
14	KAP1	chr22:29137462-29138868	U2OS	brain:	n/a	chr22:29138409-29138417
15	SPI1	chr22:29137429-29138131	GM12878	blood:	n/a	chr22:29137736-29137749 chr22:29137738-29137747
16	MYC	chr22:29137301-29138626	K562	blood:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
17	SPI1	chr22:29137364-29138140	GM12891	blood:	n/a	chr22:29137736-29137749 chr22:29137738-29137747
18	TBL1XR1	chr22:29137455-29138694	GM12878	blood:	n/a	n/a
19	IRF4	chr22:29137416-29137977	GM12878	blood:	n/a	n/a
20	RFX5	chr22:29137339-29138017	K562	blood:	n/a	chr22:29138001-29138010 chr22:29137842-29137851
21	STAT5A	chr22:29137428-29138536	GM12878	blood:	n/a	chr22:29138327-29138347
22	JUND	chr22:29137435-29138087	MCF-7	breast:	n/a	chr22:29137748-29137755 chr22:29137748-29137757 chr22:29137843-29137852 chr22:29137492-29137502 chr22:29137746-29137757 chr22:29138002-29138011 chr22:29137751-29137759
23	TBP	chr22:29137360-29138145	Hela-S3	cervix:	n/a	n/a
24	TCF12	chr22:29137443-29138884	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr22:29137391-29138694	K562	blood:	n/a	n/a
26	JUND	chr22:29137366-29138387	H1-hESC	embryonic stem cell:	n/a	chr22:29137748-29137755 chr22:29137748-29137757 chr22:29137843-29137852 chr22:29137492-29137502 chr22:29137746-29137757 chr22:29138002-29138011 chr22:29137751-29137759
27	RELA	chr22:29137391-29138698	GM15510	blood:	n/a	n/a
28	MAZ	chr22:29137442-29138797	GM12878	blood:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
29	FOXM1	chr22:29137421-29138274	ECC-1	luminal epithelium:	n/a	n/a
30	MYC	chr22:29137389-29138740	NB4	blood:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
31	FOXM1	chr22:29137380-29138533	GM12878	blood:	n/a	n/a
32	MAX	chr22:29137362-29138840	A549	lung:	n/a	chr22:29137755-29137762 chr22:29137982-29137992
33	RUNX3	chr22:29137404-29138655	GM12878	blood:	n/a	n/a
34	IRF4	chr22:29137390-29138072	GM12878	blood:	n/a	n/a
35	POLR2A	chr22:29137394-29138612	GM12892	blood:	n/a	n/a
36	POLR2A	chr22:29137415-29138655	K562	blood:	n/a	n/a
37	POLR2A	chr22:29137431-29138424	PBDE	blood:	n/a	n/a
38	RAD21	chr22:29137360-29138069	Hela-S3	cervix:	n/a	n/a
39	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
40	POLR2A	chr22:29137448-29138925	GM19099	blood:	n/a	n/a
41	POLR2A	chr22:29137310-29139038	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr22:29137420-29137570	HFF-Myc	foreskin:	n/a	n/a
43	CREB1	chr22:29137393-29138780	GM12878	blood:	n/a	n/a
44	GTF2F1	chr22:29137442-29138061	K562	blood:	n/a	n/a
45	HCFC1	chr22:29137292-29138934	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr22:29137260-29138916	K562	blood:	n/a	n/a
47	POLR2A	chr22:29137347-29138823	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr22:29137466-29138749	PANC-1	pancreas:	n/a	n/a
49	POLR2A	chr22:29137456-29138745	HUVEC	blood vessel:	n/a	n/a
50	MAX	chr22:29137467-29138819	SK-N-SH	brain:	n/a	chr22:29137755-29137762 chr22:29137982-29137992

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	chr22:29137399..29139735-chr22:29278518..29281229,2	MCF-7	breast:
4	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
5	chr22:29137011..29139217-chr22:29662922..29665353,2	MCF-7	breast:
6	chr22:29133133..29134961-chr22:29136110..29137715,2	K562	blood:
7	chr22:29136431..29140671-chr22:29167494..29170117,5	K562	blood:
8	chr22:29134319..29139472-chr22:29186598..29194420,8	K562	blood:
9	chr14:24681489..24683896-chr22:29136971..29139325,2	MCF-7	breast:
10	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
11	chr22:29133437..29141650-chr22:29203240..29216422,34	MCF-7	breast:
12	chr22:29134224..29141746-chr22:29191206..29200044,27	MCF-7	breast:
13	chr22:29127658..29141630-chr22:29187451..29201381,67	MCF-7	breast:
14	chr22:29124921..29127441-chr22:29136398..29138709,2	K562	blood:

Variant related genes	Relation type
HSCB	TF binding region
ENSG00000100219	Chromatin interaction
ENSG00000182944	Chromatin interaction
ENSG00000272858	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000183579	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000159873	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000254692	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17880353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17880459	0.80[AFR][1000 genomes]
rs17881056	0.80[AFR][1000 genomes]
rs17883144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17884212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17885109	0.80[AFR][1000 genomes]
rs17885728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No data

Chromatin state (count:126 , 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	chr22:29136000-29139400	Active TSS	K562	blood
6	chr22:29136400-29139200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr22:29136600-29139600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr22:29136800-29138800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr22:29136800-29138800	Active TSS	GM12878-XiMat	blood
10	chr22:29136800-29138800	Active TSS	Hela-S3	cervix
11	chr22:29137000-29138000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:29137000-29138800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr22:29137000-29138800	Active TSS	HMEC	breast
14	chr22:29137000-29139400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr22:29137000-29139400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr22:29137200-29137600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:29137200-29137600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr22:29137200-29137600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr22:29137200-29137600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr22:29137200-29137600	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr22:29137200-29137600	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr22:29137200-29137600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr22:29137200-29137600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr22:29137200-29137600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr22:29137200-29137600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr22:29137200-29137600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr22:29137200-29137600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr22:29137200-29137600	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr22:29137200-29137600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr22:29137200-29137600	Flanking Active TSS	Fetal Kidney	kidney
31	chr22:29137200-29137600	Enhancers	Left Ventricle	heart
32	chr22:29137200-29137600	Flanking Active TSS	HSMM	muscle
33	chr22:29137200-29137600	Flanking Active TSS	HUVEC	blood vessel
34	chr22:29137200-29137600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr22:29137200-29137600	Flanking Active TSS	NH-A	brain
36	chr22:29137200-29137600	Flanking Active TSS	Osteobl	bone
37	chr22:29137200-29137800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr22:29137200-29137800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr22:29137200-29137800	Flanking Active TSS	Liver	Liver
40	chr22:29137200-29137800	Flanking Active TSS	Fetal Thymus	thymus
41	chr22:29137200-29137800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr22:29137200-29138800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr22:29137200-29138800	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr22:29137200-29138800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr22:29137200-29138800	Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr22:29137200-29138800	Active TSS	Muscle Satellite Cultured Cells	--
47	chr22:29137200-29138800	Active TSS	Brain Anterior Caudate	brain
48	chr22:29137200-29138800	Active TSS	Brain Germinal Matrix	brain
49	chr22:29137200-29138800	Active TSS	Colonic Mucosa	Colon
50	chr22:29137200-29138800	Active TSS	Fetal Brain Female	brain

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