Variant report

Variant	rs1153952
Chromosome Location	chr1:223958547-223958548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
2	chr1:223957411..223959662-chr1:224032167..224034658,2	MCF-7	breast:
3	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
4	chr1:223958219..223959890-chr1:224031249..224033872,2	K562	blood:
5	chr1:223950388..223952525-chr1:223958515..223960018,2	K562	blood:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction
ENSG00000143514	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	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1153928	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1153937	0.93[ASN][1000 genomes]
rs1153938	0.92[ASN][1000 genomes]
rs1153943	0.88[CHB][hapmap];0.83[JPT][hapmap];0.93[ASN][1000 genomes]
rs1153944	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153950	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	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153956	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1222081	1.00[CEU][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222123	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222126	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1222127	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222147	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222153	0.83[ASW][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1222158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228475	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538140	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17739	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982611	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60739082	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6604726	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6658724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661816	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6667215	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694471	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6698919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898878	0.89[AMR][1000 genomes];0.92[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
rs1153952	HLX	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
3	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:223954200-223958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:223954400-223958600	Weak transcription	Ovary	ovary
8	chr1:223954400-223961800	Weak transcription	HepG2	liver
9	chr1:223954800-223964000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:223956600-223958600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr1:223956600-223958600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:223956600-223958600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:223956600-223958600	Strong transcription	Colon Smooth Muscle	Colon
14	chr1:223956600-223958600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr1:223956600-223958600	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:223956600-223958600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:223956600-223958600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr1:223956600-223958600	Strong transcription	HMEC	breast
19	chr1:223956600-223958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:223956600-223958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:223956600-223958800	Weak transcription	Primary B cells from cord blood	blood
22	chr1:223956600-223958800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:223956600-223958800	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:223956600-223959000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:223956600-223959000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:223956600-223959000	Strong transcription	Brain Anterior Caudate	brain
27	chr1:223956600-223959000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr1:223956600-223959200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:223956600-223959200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:223956600-223959200	Strong transcription	Fetal Kidney	kidney
31	chr1:223956600-223959200	Strong transcription	Fetal Lung	lung
32	chr1:223956600-223959400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:223956600-223959400	Strong transcription	Rectal Smooth Muscle	rectum
34	chr1:223956600-223960000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:223956600-223960400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:223956600-223960800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr1:223956600-223962800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:223956600-223963400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:223956600-223963600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:223956600-223963600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:223956600-223963800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:223956600-223967000	Strong transcription	Lung	lung
43	chr1:223956600-223967200	Strong transcription	Colonic Mucosa	Colon
44	chr1:223956600-223968400	Strong transcription	Fetal Brain Female	brain
45	chr1:223956600-223969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:223956600-223969000	Strong transcription	Fetal Stomach	stomach
47	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr1:223956800-223958600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:223956800-223958600	Strong transcription	Fetal Intestine Large	intestine

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