Variant report

Variant	rs59509028
Chromosome Location	chr22:29977836-29977837
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr22:29977643-29978432	MCF-7	breast:	n/a	n/a
2	MAX	chr22:29977547-29977898	A549	lung:	n/a	n/a
3	GATA3	chr22:29977701-29978310	T-47D	breast:	n/a	n/a
4	GATA3	chr22:29977744-29978267	T-47D	breast:	n/a	n/a
5	MXI1	chr22:29975754-29978016	SK-N-SH	brain:	n/a	chr22:29977179-29977188
6	HDAC2	chr22:29977806-29978311	MCF-7	breast:	n/a	n/a
7	HDAC2	chr22:29977709-29978255	MCF-7	breast:	n/a	n/a
8	MAX	chr22:29977574-29978173	MCF-7	breast:	n/a	n/a
9	NR2F2	chr22:29977699-29978361	MCF-7	breast:	n/a	n/a
10	GATA3	chr22:29977628-29978470	MCF-7	breast:	n/a	n/a
11	GABPA	chr22:29977817-29978181	MCF-7	breast:	n/a	n/a
12	POLR2A	chr22:29976318-29978116	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr22:29977604-29978371	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:29975483..29978642-chr22:29996311..30000725,6	MCF-7	breast:
2	chr22:29947295..29951735-chr22:29976015..29980297,4	K562	blood:
3	chr22:29663275..29666008-chr22:29976454..29978804,2	K562	blood:
4	chr22:29948374..29951089-chr22:29975785..29978624,4	MCF-7	breast:
5	chr22:29782601..29785697-chr22:29975164..29978533,5	MCF-7	breast:
6	chr22:29975560..29978145-chr22:29998416..30001350,4	MCF-7	breast:
7	chr22:29948193..29950224-chr22:29975940..29978547,6	MCF-7	breast:

No data

Variant related genes	Relation type
NIPSNAP1	TF binding region
ENSG00000182944	Chromatin interaction
ENSG00000100263	Chromatin interaction
ENSG00000186575	Chromatin interaction
ENSG00000100280	Chromatin interaction
ENSG00000100296	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12019218	0.87[AFR][1000 genomes]
rs16987835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16987915	0.90[AFR][1000 genomes]
rs57599366	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59242053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61056759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73390907	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73390948	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1058156	chr22:29772043-30024013	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv544675	chr22:29772043-30024013	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv1062373	chr22:29826745-30092448	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv544676	chr22:29826745-30092448	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
6	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv834172	chr22:29899036-30057948	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv521852	chr22:29974831-29983138	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29976200-29978000	Active TSS	Rectal Smooth Muscle	rectum
2	chr22:29976600-29978000	Active TSS	A549	lung
3	chr22:29976800-29978200	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr22:29977200-29978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr22:29977200-29978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr22:29977400-29978000	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr22:29977400-29978000	Enhancers	Stomach Mucosa	stomach
8	chr22:29977400-29978000	Enhancers	Spleen	Spleen
9	chr22:29977400-29978200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:29977400-29978200	Enhancers	HMEC	breast
11	chr22:29977600-29978000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr22:29977600-29978000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr22:29977600-29978000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr22:29977600-29978000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr22:29977600-29978000	Enhancers	Pancreas	Pancrea
16	chr22:29977600-29978000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr22:29977600-29978000	Enhancers	Small Intestine	intestine
18	chr22:29977600-29978000	Flanking Active TSS	K562	blood
19	chr22:29977600-29978200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr22:29977600-29978200	Flanking Active TSS	Dnd41	blood
21	chr22:29977600-29978200	Flanking Active TSS	NHEK	skin
22	chr22:29977600-29979200	Enhancers	Thymus	Thymus
23	chr22:29977600-29998800	Weak transcription	Right Atrium	heart
24	chr22:29977800-29978000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr22:29977800-29978000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr22:29977800-29978000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr22:29977800-29978000	Enhancers	Primary B cells from cord blood	blood
28	chr22:29977800-29978000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr22:29977800-29978000	Enhancers	Primary hematopoietic stem cells	blood
30	chr22:29977800-29978000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr22:29977800-29978000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr22:29977800-29978000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr22:29977800-29978000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr22:29977800-29978000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr22:29977800-29978000	Enhancers	Fetal Intestine Small	intestine
36	chr22:29977800-29978200	Enhancers	Primary B cells from peripheral blood	blood
37	chr22:29977800-29978200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr22:29977800-29978200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr22:29977800-29978200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr22:29977800-29978200	Enhancers	Hela-S3	cervix
41	chr22:29977800-29978600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr22:29977800-29978800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:29977800-29979000	Enhancers	Placenta	Placenta
44	chr22:29977800-29979200	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr22:29977800-29979400	Enhancers	Fetal Thymus	thymus
46	chr22:29977800-29979400	Enhancers	HepG2	liver
47	chr22:29977800-29984000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr22:29977800-29994200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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