Variant report

Variant	rs1222123
Chromosome Location	chr1:223967237-223967238
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223964914..223967856-chr1:224032399..224034591,2	K562	blood:
2	chr1:223935650..223937154-chr1:223966505..223968008,2	MCF-7	breast:
3	chr1:223963678..223965636-chr1:223966961..223968490,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1003061	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1153928	0.96[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	0.93[ASN][1000 genomes]
rs1153944	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1153946	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153950	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153952	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153954	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1153956	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1222081	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1222126	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1222127	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222147	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222148	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222153	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1222158	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1228475	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1538140	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17739	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982611	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60739082	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6604726	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6658724	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6661816	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6667215	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6694471	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6698919	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs898878	0.90[AMR][1000 genomes];0.95[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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-223968400	Strong transcription	Fetal Brain Female	brain
2	chr1:223956600-223969000	Strong transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:223956600-223969000	Strong transcription	Fetal Stomach	stomach
4	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr1:223956800-223969000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:223956800-223969200	Strong transcription	Placenta	Placenta
8	chr1:223956800-223974200	Strong transcription	Primary T cells from cord blood	blood
9	chr1:223956800-223974200	Strong transcription	Liver	Liver
10	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:223957200-223968000	Strong transcription	Brain Germinal Matrix	brain
12	chr1:223957200-223968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:223957200-223972800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr1:223959600-223969000	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr1:223960000-223968600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:223960000-223969000	Strong transcription	Fetal Kidney	kidney
18	chr1:223960000-223972200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:223960200-223970000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:223960200-223971800	Strong transcription	Stomach Smooth Muscle	stomach
21	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
22	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr1:223960400-223968800	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:223960800-223967400	Strong transcription	Brain Cingulate Gyrus	brain
28	chr1:223960800-223967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:223960800-223968600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
31	chr1:223961200-223968400	Strong transcription	Fetal Lung	lung
32	chr1:223961400-223968800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:223961400-223969000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:223961600-223968000	Strong transcription	Brain Anterior Caudate	brain
35	chr1:223961800-223969000	Strong transcription	Rectal Smooth Muscle	rectum
36	chr1:223961800-223972200	Strong transcription	Dnd41	blood
37	chr1:223961800-223977200	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:223962000-223975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:223962600-223970600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:223962600-223983600	Weak transcription	Psoas Muscle	Psoas
42	chr1:223962800-223972600	Strong transcription	Primary B cells from cord blood	blood
43	chr1:223963000-223968400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:223963200-223969000	Strong transcription	Ovary	ovary
45	chr1:223963400-223983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:223963600-223968400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:223963600-223969000	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr1:223963800-223969200	Strong transcription	Thymus	Thymus
49	chr1:223964000-223972200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:223964000-223985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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