Variant report

Variant	rs10919267
Chromosome Location	chr1:169861212-169861213
allele	C/T
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	POLR2A	chr1:169861160-169864335	GM12878	blood:	n/a	n/a
2	GATA3	chr1:169860320-169861222	MCF-7	breast:	n/a	chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860854-169860861 chr1:169860852-169860862 chr1:169860852-169860861

No.	Distal block	Cell Line	Cell type
1	chr1:169704931..169706505-chr1:169859799..169862220,2	K562	blood:
2	chr1:169763198..169765886-chr1:169860155..169862900,4	K562	blood:
3	chr1:169847953..169852057-chr1:169858381..169863040,5	MCF-7	breast:
4	chr1:169708422..169710485-chr1:169860930..169862840,2	MCF-7	breast:
5	chr1:169845717..169848182-chr1:169860925..169862962,2	MCF-7	breast:
6	chr1:169764521..169766056-chr1:169860447..169863119,2	MCF-7	breast:
7	chr1:169770089..169773107-chr1:169860421..169863060,3	K562	blood:
8	chr1:169763198..169765715-chr1:169860443..169862900,3	K562	blood:

Variant related genes	Relation type
SCYL3	TF binding region
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10458398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10489172	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1062976	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10800487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10919250	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10919255	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10919268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10919269	0.84[ASN][1000 genomes]
rs11576078	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11589247	0.94[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12023729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12024570	0.84[ASN][1000 genomes]
rs12025296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12027790	0.84[ASN][1000 genomes]
rs12035711	0.84[ASN][1000 genomes]
rs12036824	1.00[JPT][hapmap]
rs12044536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12064636	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12066551	0.84[ASN][1000 genomes]
rs12077708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12083317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12089057	0.80[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12760399	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16862745	0.94[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17529513	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17603022	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2103641	0.84[ASN][1000 genomes]
rs2272912	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2272915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs35296671	0.82[EUR][1000 genomes]
rs4987342	1.00[JPT][hapmap]
rs516793	0.83[EUR][1000 genomes]
rs549002	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs621437	0.83[EUR][1000 genomes]
rs648576	0.82[EUR][1000 genomes]
rs659476	0.83[EUR][1000 genomes]
rs6678351	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6694855	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73026213	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73026223	0.82[AMR][1000 genomes]
rs73026243	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73026245	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7531947	0.84[ASN][1000 genomes]
rs7532990	0.84[ASN][1000 genomes]
rs7533350	0.84[ASN][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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169786200-169862400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:169845200-169861400	Weak transcription	Right Ventricle	heart
3	chr1:169845200-169861400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:169845400-169861400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:169851600-169861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:169852600-169861400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:169852600-169861400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:169852600-169862200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:169852800-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:169853800-169861400	Weak transcription	Fetal Stomach	stomach
11	chr1:169855000-169861400	Weak transcription	HSMMtube	muscle
12	chr1:169855400-169861400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:169856000-169861400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:169856000-169861400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:169856200-169861400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:169857400-169861400	Weak transcription	Fetal Brain Female	brain
17	chr1:169858000-169861400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:169858000-169861400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:169858000-169861400	Weak transcription	Fetal Brain Male	brain
20	chr1:169858000-169861400	Weak transcription	K562	blood
21	chr1:169858200-169861400	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr1:169858200-169861400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:169858800-169861600	Enhancers	Small Intestine	intestine
24	chr1:169859000-169861400	Enhancers	Fetal Lung	lung
25	chr1:169859000-169861400	Enhancers	Dnd41	blood
26	chr1:169859000-169861800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr1:169859000-169861800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:169859400-169861400	Weak transcription	Left Ventricle	heart
29	chr1:169859400-169862000	Weak transcription	Ovary	ovary
30	chr1:169859600-169861600	Enhancers	Fetal Intestine Small	intestine
31	chr1:169859800-169861400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:169859800-169861400	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr1:169859800-169861400	Enhancers	Thymus	Thymus
34	chr1:169859800-169861600	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:169859800-169861600	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:169859800-169861600	Enhancers	Brain Anterior Caudate	brain
37	chr1:169860000-169861400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:169860000-169861400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:169860000-169861400	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:169860000-169861400	Enhancers	Adipose Nuclei	Adipose
41	chr1:169860000-169861400	Enhancers	Colon Smooth Muscle	Colon
42	chr1:169860000-169861400	Enhancers	Stomach Smooth Muscle	stomach
43	chr1:169860000-169861600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:169860000-169861600	Enhancers	Primary hematopoietic stem cells	blood
45	chr1:169860000-169861600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:169860000-169861600	Enhancers	Brain Substantia Nigra	brain
47	chr1:169860000-169861600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr1:169860000-169861600	Enhancers	Fetal Intestine Large	intestine
49	chr1:169860000-169861600	Enhancers	Fetal Thymus	thymus
50	chr1:169860000-169861600	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links