Variant report

Variant	rs720621
Chromosome Location	chr22:28313583-28313584
allele	A/C
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	MXI1	chr22:28313485-28316548	IMR90	lung:	n/a	n/a
2	MYC	chr22:28313570-28315642	MCF10A-Er-Src	breast:	n/a	chr22:28314497-28314510 chr22:28314497-28314507 chr22:28314501-28314508 chr22:28314497-28314510 chr22:28314495-28314510 chr22:28315026-28315036 chr22:28314497-28314512 chr22:28314905-28314914 chr22:28314498-28314509 chr22:28314498-28314509 chr22:28314498-28314508 chr22:28314497-28314510 chr22:28314499-28314508
3	POLR2A	chr22:28313255-28316499	MCF10A-Er-Src	breast:	n/a	n/a
4	MXI1	chr22:28312696-28316713	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:28309562..28313647-chr22:28313905..28316499,4	MCF-7	breast:
2	chr22:28296920..28299668-chr22:28312010..28313621,2	K562	blood:

Variant related genes	Relation type
TTC28-AS1	TF binding region
ENSG00000235954	Chromatin interaction
ENSG00000180957	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs138631	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs138638	0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[TSI][hapmap]
rs138650	0.80[CHD][hapmap];0.85[TSI][hapmap]
rs138685	0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1548235	0.80[CHD][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap]
rs2038158	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2267121	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2267124	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3747141	0.80[CHD][hapmap]
rs4140571	0.85[CHD][hapmap];0.84[TSI][hapmap]
rs470100	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs470105	0.82[MEX][hapmap]
rs5752667	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs5762393	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5762416	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5762418	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs5997319	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6005671	0.89[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73425788	0.85[ASN][1000 genomes]
rs738451	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738453	0.84[CEU][hapmap]
rs957601	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv588878	chr22:28248840-28314113	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs720621	MED30	trans	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28295200-28313800	Weak transcription	Colonic Mucosa	Colon
2	chr22:28298400-28314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:28299200-28314000	Weak transcription	Spleen	Spleen
4	chr22:28306400-28313800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr22:28306400-28313800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:28306400-28314200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr22:28306400-28314400	Weak transcription	Esophagus	oesophagus
8	chr22:28306600-28313800	Weak transcription	Lung	lung
9	chr22:28307000-28313800	Weak transcription	Fetal Thymus	thymus
10	chr22:28307200-28313600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr22:28307200-28313800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr22:28307200-28313800	Weak transcription	Placenta	Placenta
13	chr22:28308000-28313800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr22:28308000-28314000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr22:28308200-28313800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr22:28309200-28313600	Enhancers	HepG2	liver
17	chr22:28309800-28313600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr22:28309800-28313600	Weak transcription	Thymus	Thymus
19	chr22:28309800-28313800	Enhancers	Liver	Liver
20	chr22:28309800-28313800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr22:28310000-28313600	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr22:28310000-28313600	Weak transcription	Brain Anterior Caudate	brain
23	chr22:28310000-28313600	Weak transcription	Right Ventricle	heart
24	chr22:28310000-28313800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr22:28310000-28313800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr22:28310000-28313800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr22:28310000-28313800	Weak transcription	Left Ventricle	heart
28	chr22:28310000-28313800	Weak transcription	Pancreas	Pancrea
29	chr22:28310000-28313800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:28310200-28313600	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr22:28310200-28313600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr22:28310200-28313800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr22:28310600-28313800	Enhancers	Fetal Heart	heart
34	chr22:28310600-28313800	Weak transcription	HSMMtube	muscle
35	chr22:28310800-28313800	Weak transcription	Fetal Intestine Large	intestine
36	chr22:28310800-28314000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr22:28311200-28316200	Active TSS	GM12878-XiMat	blood
38	chr22:28311400-28313600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr22:28311400-28314400	Enhancers	Small Intestine	intestine
40	chr22:28311600-28314000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr22:28311800-28314000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr22:28312000-28313600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr22:28312000-28313600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr22:28312000-28313600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr22:28312000-28313600	Weak transcription	Fetal Kidney	kidney
46	chr22:28312000-28313600	Weak transcription	Ovary	ovary
47	chr22:28312000-28314000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr22:28312200-28313800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr22:28312200-28313800	Active TSS	Breast Myoepithelial Primary Cells	Breast
50	chr22:28312200-28313800	Weak transcription	Gastric	stomach

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