Variant report

Variant	rs10494938
Chromosome Location	chr1:211848035-211848036
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	E2F4	chr1:211847458-211849574	MCF10A-Er-Src	breast:	n/a	n/a
2	RCOR1	chr1:211847989-211849492	Hela-S3	cervix:	n/a	n/a
3	CUX1	chr1:211847759-211848063	K562	blood:	n/a	n/a
4	JUN	chr1:211847760-211849648	K562	blood:	n/a	chr1:211849021-211849030

No.	Distal block	Cell Line	Cell type
1	chr1:211843019..211845413-chr1:211846374..211848527,3	MCF-7	breast:
2	chr1:211736674..211739531-chr1:211847084..211848830,2	K562	blood:
3	chr1:211751583..211753296-chr1:211847712..211850652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231057	TF binding region
NEK2	TF binding region
ENSG00000117650	Chromatin interaction
ENSG00000170385	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10494940	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17651870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2083903	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35573429	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275370	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828229	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61828230	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61849678	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61849681	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61849682	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61849684	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61849685	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6697046	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6704128	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

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	esv2754845	chr1:211846605-211878605	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211829600-211848600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:211841000-211848400	Weak transcription	Stomach Mucosa	stomach
3	chr1:211841400-211848200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:211842000-211848400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:211844200-211848400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:211844400-211848200	Weak transcription	Fetal Intestine Large	intestine
7	chr1:211846400-211848400	Weak transcription	Small Intestine	intestine
8	chr1:211847400-211848200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:211847400-211848200	Flanking Active TSS	K562	blood
10	chr1:211847400-211848400	Flanking Active TSS	Hela-S3	cervix
11	chr1:211847400-211848400	Flanking Active TSS	HepG2	liver
12	chr1:211847600-211848200	Flanking Active TSS	A549	lung
13	chr1:211847600-211848400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:211847600-211848400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:211847600-211848400	Enhancers	Primary B cells from cord blood	blood
16	chr1:211847600-211848400	Active TSS	Fetal Brain Female	brain
17	chr1:211847600-211848600	Flanking Active TSS	NHEK	skin
18	chr1:211847600-211848600	Flanking Active TSS	NHLF	lung
19	chr1:211847600-211848800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:211847600-211848800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr1:211847600-211848800	Flanking Active TSS	HMEC	breast
22	chr1:211847600-211848800	Flanking Active TSS	Osteobl	bone
23	chr1:211847600-211849400	Flanking Active TSS	HUVEC	blood vessel
24	chr1:211847600-211850000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:211847600-211850000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:211847600-211850000	Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr1:211847800-211848200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
28	chr1:211847800-211848200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:211847800-211848200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:211847800-211848200	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:211847800-211848400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:211847800-211848400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:211847800-211848400	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr1:211847800-211848400	Enhancers	Primary hematopoietic stem cells	blood
35	chr1:211847800-211848600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr1:211847800-211848600	Flanking Active TSS	Fetal Heart	heart
37	chr1:211847800-211848600	Flanking Active TSS	Dnd41	blood
38	chr1:211847800-211848800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr1:211847800-211848800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr1:211847800-211849600	Active TSS	Fetal Kidney	kidney
41	chr1:211847800-211849600	Active TSS	NHDF-Ad	bronchial
42	chr1:211847800-211849800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:211848000-211848200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr1:211848000-211848200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:211848000-211848200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:211848000-211848200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:211848000-211848200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:211848000-211848200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:211848000-211848200	Enhancers	Primary T cells from cord blood	blood
50	chr1:211848000-211848200	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links