Variant report

Variant	rs6425310
Chromosome Location	chr1:174971682-174971683
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:174971149-174971691	K562	blood:	n/a	chr1:174971341-174971352
2	POLR2A	chr1:174963970-174972111	K562	blood:	n/a	n/a
3	CTCF	chr1:174971560-174971710	HMF	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174968752..174972930-chr1:174980465..174984788,7	MCF-7	breast:
2	chr1:173835653..173838766-chr1:174968504..174972418,4	K562	blood:
3	chr1:174966465..174968007-chr1:174970965..174973643,2	MCF-7	breast:
4	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
5	chr1:174968308..174972682-chr1:174973669..174977278,7	MCF-7	breast:
6	chr1:174966903..174971287-chr1:174971534..174977740,10	MCF-7	breast:

No data

Variant related genes	Relation type
CACYBP	TF binding region
ENSG00000116161	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000120333	Chromatin interaction
ENSG00000206659	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1046439	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11590474	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs1754355	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs1801791	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1978053	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1984418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2105949	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2187562	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs2187939	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285208	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2285210	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301507	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2987869	0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs3018410	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap]
rs3133270	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs35996757	0.85[ASN][1000 genomes]
rs3753563	0.91[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap]
rs4233195	0.91[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap]
rs4651238	0.91[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap]
rs6425305	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs6425309	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665216	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs6669560	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7514888	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538588	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs9804056	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap]
rs989423	0.91[CHB][hapmap];0.87[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425310	SLC9A11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174968200-174971800	Active TSS	K562	blood
2	chr1:174969800-174972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:174969800-174981600	Weak transcription	Gastric	stomach
4	chr1:174970000-174974000	Weak transcription	Left Ventricle	heart
5	chr1:174970000-174977000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:174970000-174977200	Weak transcription	Lung	lung
7	chr1:174970000-174977200	Weak transcription	Pancreas	Pancrea
8	chr1:174970000-174982400	Weak transcription	Esophagus	oesophagus
9	chr1:174970000-174991800	Weak transcription	Stomach Mucosa	stomach
10	chr1:174970200-174971800	Enhancers	Fetal Heart	heart
11	chr1:174970200-174972000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:174970200-174973800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:174970200-174976600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:174970200-174977000	Weak transcription	Colonic Mucosa	Colon
15	chr1:174970200-174981200	Weak transcription	Right Ventricle	heart
16	chr1:174970400-174971800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:174970400-174971800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:174970400-174972000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:174970400-174972000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr1:174970400-174972200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:174970400-174972200	Enhancers	Adipose Nuclei	Adipose
22	chr1:174970400-174972200	Weak transcription	Psoas Muscle	Psoas
23	chr1:174970400-174973000	Enhancers	Liver	Liver
24	chr1:174970400-174973200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:174970400-174973800	Weak transcription	Fetal Intestine Large	intestine
26	chr1:174970400-174976800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:174970400-174977200	Weak transcription	Aorta	Aorta
28	chr1:174970600-174971800	Flanking Active TSS	Hela-S3	cervix
29	chr1:174970600-174972000	Enhancers	Primary B cells from cord blood	blood
30	chr1:174970600-174972200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:174970600-174972600	Enhancers	Fetal Thymus	thymus
32	chr1:174970600-174973200	Enhancers	Small Intestine	intestine
33	chr1:174970600-174973600	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr1:174970600-174974000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:174970600-174977200	Weak transcription	Fetal Stomach	stomach
36	chr1:174970600-174981800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:174970800-174971800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr1:174970800-174971800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:174970800-174971800	Enhancers	HMEC	breast
40	chr1:174970800-174971800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr1:174970800-174972000	Enhancers	Fetal Intestine Small	intestine
42	chr1:174970800-174972200	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr1:174970800-174972200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:174970800-174972200	Weak transcription	Ovary	ovary
45	chr1:174970800-174972200	Enhancers	Osteobl	bone
46	chr1:174970800-174972400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:174970800-174972600	Enhancers	Primary T cells from cord blood	blood
48	chr1:174970800-174972600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:174970800-174972600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:174970800-174973000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links