Variant report

Variant	rs1153950
Chromosome Location	chr1:223959796-223959797
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223958981..223961667-chr1:224244026..224246906,2	K562	blood:
2	chr1:223959045..223962573-chr1:223982602..223986038,3	K562	blood:
3	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
4	chr1:223958219..223959890-chr1:224031249..224033872,2	K562	blood:
5	chr1:223947284..223949321-chr1:223959438..223962794,3	K562	blood:
6	chr1:223950388..223952525-chr1:223958515..223960018,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1003061	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153928	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153937	0.93[ASN][1000 genomes]
rs1153938	0.92[ASN][1000 genomes]
rs1153943	0.83[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs1153944	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153946	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153952	0.83[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153954	0.82[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153956	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1222081	0.91[CEU][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222123	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222126	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1222127	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222147	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222148	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222153	0.89[CHB][hapmap];0.88[GIH][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1222158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228475	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538140	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17739	0.83[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982611	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60739082	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6604726	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6658724	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661816	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6667215	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694471	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6698919	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898878	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1153950	HLX	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
2	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:223954400-223961800	Weak transcription	HepG2	liver
4	chr1:223954800-223964000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:223956600-223960000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:223956600-223960400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:223956600-223960800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
8	chr1:223956600-223962800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:223956600-223963400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:223956600-223963600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:223956600-223963600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:223956600-223963800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr1:223956600-223967000	Strong transcription	Lung	lung
14	chr1:223956600-223967200	Strong transcription	Colonic Mucosa	Colon
15	chr1:223956600-223968400	Strong transcription	Fetal Brain Female	brain
16	chr1:223956600-223969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:223956600-223969000	Strong transcription	Fetal Stomach	stomach
18	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:223956800-223963000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:223956800-223963200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:223956800-223969000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:223956800-223969200	Strong transcription	Placenta	Placenta
24	chr1:223956800-223974200	Strong transcription	Primary T cells from cord blood	blood
25	chr1:223956800-223974200	Strong transcription	Liver	Liver
26	chr1:223957000-223962400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:223957000-223964000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:223957200-223965000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:223957200-223968000	Strong transcription	Brain Germinal Matrix	brain
31	chr1:223957200-223968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:223957200-223972800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:223957400-223960600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:223957400-223960800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:223957400-223962200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:223957600-223960800	Enhancers	Right Atrium	heart
37	chr1:223957800-223960200	Weak transcription	Fetal Thymus	thymus
38	chr1:223957800-223961000	Genic enhancers	NHLF	lung
39	chr1:223958000-223960800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr1:223958200-223960800	Genic enhancers	Adipose Nuclei	Adipose
41	chr1:223958200-223961000	Genic enhancers	Stomach Mucosa	stomach
42	chr1:223958200-223961200	Weak transcription	Psoas Muscle	Psoas
43	chr1:223958200-223961400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:223958200-223962000	Strong transcription	Pancreas	Pancrea
45	chr1:223958400-223960400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
46	chr1:223958400-223960800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr1:223958400-223960800	Genic enhancers	NHDF-Ad	bronchial
48	chr1:223958400-223961000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:223958400-223962000	Genic enhancers	Left Ventricle	heart
50	chr1:223958400-223963000	Genic enhancers	Skeletal Muscle Male	skeletal muscle

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