Variant report

Variant	rs7574389
Chromosome Location	chr2:86670564-86670565
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:86670537..86672265-chr2:86924211..86926595,2	MCF-7	breast:
2	chr2:86669725..86671528-chr2:86682298..86684898,2	MCF-7	breast:
3	chr2:86669498..86671776-chr2:86849448..86851643,2	MCF-7	breast:
4	chr2:86667867..86670714-chr2:86788591..86792016,6	K562	blood:
5	chr2:86667181..86671352-chr2:86788569..86792016,9	K562	blood:
6	chr2:86667874..86671580-chr2:86848738..86852940,5	K562	blood:
7	chr2:86670380..86672664-chr2:86788557..86791421,2	MCF-7	breast:
8	chr2:86668149..86671762-chr2:86690412..86696565,6	K562	blood:

No data

Variant related genes	Relation type
ENSG00000228363	Chromatin interaction
ENSG00000115548	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000115561	Chromatin interaction
ENSG00000249884	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10185085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036940	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs11127040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1116326	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11690696	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11693352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11903855	1.00[CHB][hapmap]
rs12475983	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476666	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995117	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1468039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1518811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2139150	1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218060	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2367575	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs308901	0.87[CHD][hapmap]
rs308907	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs308913	1.00[JPT][hapmap]
rs396354	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs433655	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4832284	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832287	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832288	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832290	0.95[CEU][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832293	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832294	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547688	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547689	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547690	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547700	0.87[CHD][hapmap]
rs6710124	1.00[CHB][hapmap]
rs6714826	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs6742018	1.00[JPT][hapmap];0.87[YRI][hapmap]
rs683139	0.87[CHD][hapmap]
rs7598058	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966477	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7574389	RNF103	cis	cerebellum	SCAN
rs7574389	ST3GAL5	cis	parietal	SCAN
rs7574389	KDM3A	cis	parietal	SCAN
rs7574389	IMMT	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86667600-86670800	Active TSS	Colonic Mucosa	Colon
2	chr2:86667800-86670600	Active TSS	Psoas Muscle	Psoas
3	chr2:86667800-86671200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:86668000-86670600	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr2:86668000-86670600	Active TSS	Aorta	Aorta
6	chr2:86668600-86671200	Active TSS	Right Atrium	heart
7	chr2:86669200-86670800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr2:86669200-86672000	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr2:86669400-86670600	Flanking Active TSS	Liver	Liver
10	chr2:86669400-86670800	Transcr. at gene 5' and 3'	K562	blood
11	chr2:86669400-86671000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:86669400-86671600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:86669600-86670600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr2:86669600-86670600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr2:86669800-86670600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr2:86669800-86670600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr2:86669800-86670800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:86669800-86670800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:86669800-86671000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:86669800-86671000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr2:86669800-86671000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:86669800-86671000	Flanking Active TSS	Hela-S3	cervix
23	chr2:86669800-86671800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:86669800-86671800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr2:86669800-86678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:86669800-86679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:86670000-86670600	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr2:86670000-86670600	Weak transcription	Esophagus	oesophagus
29	chr2:86670000-86670600	Active TSS	Fetal Brain Male	brain
30	chr2:86670000-86670600	Weak transcription	Placenta	Placenta
31	chr2:86670000-86670600	Flanking Active TSS	A549	lung
32	chr2:86670000-86670600	Flanking Active TSS	HMEC	breast
33	chr2:86670000-86670600	Flanking Active TSS	NH-A	brain
34	chr2:86670000-86670600	Flanking Active TSS	NHDF-Ad	bronchial
35	chr2:86670000-86670600	Flanking Active TSS	Osteobl	bone
36	chr2:86670000-86670800	Weak transcription	Lung	lung
37	chr2:86670000-86670800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr2:86670000-86670800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:86670000-86671000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:86670000-86671000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
41	chr2:86670000-86671400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr2:86670000-86671600	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr2:86670000-86671600	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr2:86670000-86671600	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:86670000-86672800	Enhancers	Small Intestine	intestine
46	chr2:86670000-86678200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr2:86670000-86684200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr2:86670200-86670600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:86670200-86670600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:86670200-86670600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links