Variant report

Variant	rs41281603
Chromosome Location	chr22:29168587-29168588
allele	C/G
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	EP300	chr22:29168435-29168873	SK-N-SH_RA	brain:	n/a	n/a
2	YY1	chr22:29168257-29169323	GM12892	blood:	n/a	chr22:29168772-29168783 chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168796-29168810 chr22:29168590-29168612 chr22:29168768-29168782
3	YY1	chr22:29168433-29168729	HCT-116	colon:	n/a	chr22:29168640-29168651 chr22:29168588-29168607 chr22:29168593-29168601 chr22:29168590-29168600 chr22:29168590-29168612
4	MAX	chr22:29168464-29168870	NB4	blood:	n/a	n/a
5	POLR2A	chr22:29168424-29169821	GM18505	blood:	n/a	n/a
6	MYBL2	chr22:29168334-29168857	HepG2	liver:	n/a	n/a
7	CTCF	chr22:29168560-29168710	SAEC	small airway:	n/a	n/a
8	TAF1	chr22:29168434-29168884	H1-neurons	neurons:	n/a	n/a
9	RFX5	chr22:29168492-29168827	Hela-S3	cervix:	n/a	n/a
10	UBTF	chr22:29168426-29169632	K562	blood:	n/a	n/a
11	HDAC2	chr22:29168561-29168751	K562	blood:	n/a	n/a
12	MBD4	chr22:29168336-29168918	HepG2	liver:	n/a	n/a
13	POLR2A	chr22:29168507-29168953	GM10847	blood:	n/a	n/a
14	MAX	chr22:29168340-29169061	HepG2	liver:	n/a	n/a
15	SIX5	chr22:29168422-29168881	GM12878	blood:	n/a	n/a
16	SIN3AK20	chr22:29168401-29168910	MCF-7	breast:	n/a	n/a
17	EP300	chr22:29168440-29168842	GM12878	blood:	n/a	n/a
18	MXI1	chr22:29168376-29168797	K562	blood:	n/a	n/a
19	POLR2A	chr22:29168307-29169740	HUVEC	blood vessel:	n/a	n/a
20	SIX5	chr22:29168451-29168806	H1-hESC	embryonic stem cell:	n/a	n/a
21	ELF1	chr22:29168314-29169052	MCF-7	breast:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
22	TAF1	chr22:29168431-29168795	GM12891	blood:	n/a	n/a
23	FOXP2	chr22:29168495-29169034	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr22:29168412-29169024	U87	brain:	n/a	n/a
25	MXI1	chr22:29168435-29169744	Hela-S3	cervix:	n/a	n/a
26	MAX	chr22:29168443-29168970	A549	lung:	n/a	n/a
27	POLR2A	chr22:29168445-29169000	HEK293	kidney:	n/a	n/a
28	CHD2	chr22:29168471-29168834	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr22:29168463-29168808	SK-N-SH_RA	brain:	n/a	n/a
30	POLR2A	chr22:29168502-29168909	HepG2	liver:	n/a	n/a
31	JUND	chr22:29168567-29168732	H1-hESC	embryonic stem cell:	n/a	n/a
32	MXI1	chr22:29168340-29170168	IMR90	lung:	n/a	n/a
33	ELF1	chr22:29168403-29168868	HepG2	liver:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
34	TAF1	chr22:29168330-29168913	PFSK-1	brain:	n/a	n/a
35	POLR2A	chr22:29168546-29169843	IMR90	lung:	n/a	n/a
36	NFIC	chr22:29168390-29168878	HepG2	liver:	n/a	n/a
37	MAX	chr22:29168402-29168956	SK-N-SH	brain:	n/a	n/a
38	MAX	chr22:29168406-29169003	MCF-7	breast:	n/a	n/a
39	SIN3AK20	chr22:29168495-29169162	K562	blood:	n/a	n/a
40	CTCF	chr22:29168583-29168751	Spleen_OC	spleen:	n/a	n/a
41	POLR2A	chr22:29168375-29169809	Raji	blood:	n/a	n/a
42	CTCF	chr22:29168580-29168730	SK-N-SH_RA	brain:	n/a	n/a
43	E2F4	chr22:29168517-29168867	MCF10A-Er-Src	breast:	n/a	n/a
44	SIN3AK20	chr22:29168555-29168746	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr22:29168504-29169683	GM19193	blood:	n/a	n/a
46	FOXA2	chr22:29168490-29168776	HepG2	liver:	n/a	n/a
47	ELK1	chr22:29168394-29168849	GM12878	blood:	n/a	n/a
48	MAX	chr22:29168487-29168812	H1-hESC	embryonic stem cell:	n/a	n/a
49	ELF1	chr22:29168289-29168990	SK-N-SH	brain:	n/a	chr22:29168639-29168648 chr22:29168800-29168812
50	GABPA	chr22:29168539-29168807	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:45660389..45661266-chr22:29168540..29169241,2	Hela-S3	cervix:
2	chr22:29165808..29174203-chr22:29186827..29200037,34	MCF-7	breast:
3	chr22:29168270..29171327-chr22:29194850..29198169,6	MCF-7	breast:
4	chr22:29136431..29140671-chr22:29167494..29170117,5	K562	blood:
5	chr22:29166664..29171376-chr22:29189061..29194611,6	MCF-7	breast:
6	chr22:29167233..29170944-chr22:29195431..29200472,7	K562	blood:
7	chr22:29134226..29139597-chr22:29164663..29170736,9	K562	blood:
8	chr22:29135038..29141691-chr22:29167545..29172967,16	MCF-7	breast:
9	chr22:29167147..29172880-chr22:29212986..29217151,7	MCF-7	breast:
10	chr22:29134212..29140528-chr22:29167074..29172462,20	MCF-7	breast:
11	chr22:29167462..29171106-chr22:29208719..29213065,6	MCF-7	breast:

Variant related genes	Relation type
CCDC117	TF binding region
ENSG00000100209	Chromatin interaction
ENSG00000160223	Chromatin interaction
ENSG00000272858	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10427858	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12330071	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17880929	1.00[AFR][1000 genomes]
rs2206061	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228260	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56119508	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997401	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005861	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6005870	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6005874	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6005898	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005899	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6005923	0.86[EUR][1000 genomes]
rs6005924	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6005926	0.86[EUR][1000 genomes]
rs9306460	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9625551	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9625565	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625575	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9625580	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29165800-29168600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr22:29167000-29168600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr22:29167600-29168600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr22:29167800-29168600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr22:29168000-29168600	Weak transcription	Lung	lung
6	chr22:29168200-29168600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr22:29168200-29168600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr22:29168200-29168600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr22:29168200-29168600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr22:29168200-29168600	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr22:29168200-29168600	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr22:29168200-29168600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
13	chr22:29168200-29168600	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr22:29168200-29168600	Enhancers	Fetal Thymus	thymus
15	chr22:29168200-29168600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr22:29168200-29168600	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr22:29168200-29168600	Flanking Active TSS	Dnd41	blood
18	chr22:29168200-29168600	Flanking Active TSS	Hela-S3	cervix
19	chr22:29168200-29168600	Flanking Active TSS	NHEK	skin
20	chr22:29168200-29169400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr22:29168200-29169400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:29168200-29169400	Active TSS	Brain Angular Gyrus	brain
23	chr22:29168200-29169400	Active TSS	Brain Cingulate Gyrus	brain
24	chr22:29168200-29169400	Active TSS	Fetal Muscle Leg	muscle
25	chr22:29168200-29169400	Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr22:29168200-29169400	Active TSS	Monocytes-CD14+_RO01746	blood
27	chr22:29168200-29169600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr22:29168200-29169600	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr22:29168200-29169600	Active TSS	K562	blood
30	chr22:29168200-29169800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr22:29168200-29169800	Active TSS	Brain Hippocampus Middle	brain
32	chr22:29168200-29169800	Active TSS	Rectal Smooth Muscle	rectum
33	chr22:29168200-29169800	Active TSS	Small Intestine	intestine
34	chr22:29168200-29169800	Active TSS	HSMMtube	muscle
35	chr22:29168200-29170000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr22:29168200-29170000	Active TSS	Right Atrium	heart
37	chr22:29168200-29170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr22:29168200-29170600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr22:29168400-29168600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr22:29168400-29168600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr22:29168400-29168600	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr22:29168400-29168600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr22:29168400-29168600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
44	chr22:29168400-29168600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr22:29168400-29168600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr22:29168400-29168600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr22:29168400-29168600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr22:29168400-29168600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr22:29168400-29168600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
50	chr22:29168400-29168600	Flanking Active TSS	Liver	Liver

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