Variant report

Variant	rs2272912
Chromosome Location	chr1:169842821-169842822
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169816798..169818330-chr1:169841352..169844284,2	MCF-7	breast:
2	chr1:169837277..169839555-chr1:169841347..169844227,3	MCF-7	breast:
3	chr1:169841592..169844397-chr1:169861385..169863350,2	K562	blood:
4	chr1:169841646..169845084-chr1:169857694..169862794,6	MCF-7	breast:
5	chr1:169837054..169838824-chr1:169842629..169844274,2	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10458398	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800487	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10919268	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919269	1.00[ASN][1000 genomes]
rs10919276	1.00[EUR][1000 genomes]
rs10919288	1.00[EUR][1000 genomes]
rs10919294	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10919295	1.00[EUR][1000 genomes]
rs10919296	1.00[EUR][1000 genomes]
rs12023729	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12024570	1.00[ASN][1000 genomes]
rs12025296	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027790	1.00[ASN][1000 genomes]
rs12035711	1.00[ASN][1000 genomes]
rs12036824	0.82[GIH][hapmap]
rs12044536	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12071325	1.00[EUR][1000 genomes]
rs12076018	1.00[EUR][1000 genomes]
rs12077708	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12079608	1.00[EUR][1000 genomes]
rs12083317	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12090220	1.00[EUR][1000 genomes]
rs12095784	1.00[EUR][1000 genomes]
rs13374781	1.00[EUR][1000 genomes]
rs13375701	1.00[EUR][1000 genomes]
rs16862886	1.00[EUR][1000 genomes]
rs16862978	1.00[EUR][1000 genomes]
rs2103641	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272915	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2901261	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3790406	1.00[JPT][hapmap]
rs4279900	1.00[EUR][1000 genomes]
rs4987370	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4987382	1.00[TSI][hapmap]
rs56084868	1.00[EUR][1000 genomes]
rs57038529	1.00[EUR][1000 genomes]
rs73041439	1.00[EUR][1000 genomes]
rs74121797	1.00[EUR][1000 genomes]
rs74122312	1.00[EUR][1000 genomes]
rs74122421	1.00[EUR][1000 genomes]
rs74122422	1.00[EUR][1000 genomes]
rs74122452	1.00[EUR][1000 genomes]
rs7531947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532990	1.00[ASN][1000 genomes]
rs7533350	1.00[ASN][1000 genomes]
rs989054	1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv872542	chr1:169802760-169844093	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 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	chr1:169805400-169848800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:169806600-169860000	Weak transcription	Stomach Mucosa	stomach
4	chr1:169814400-169848600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr1:169814600-169843200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:169814800-169848000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:169815000-169845200	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr1:169815200-169843000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:169815200-169848200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:169815400-169848400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:169817800-169848600	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
13	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:169819400-169847000	Strong transcription	Liver	Liver
15	chr1:169820400-169844800	Strong transcription	Duodenum Smooth Muscle	Duodenum
16	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169820600-169843000	Strong transcription	Primary T cells from cord blood	blood
18	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
22	chr1:169821600-169845200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr1:169822000-169846000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:169822600-169843000	Strong transcription	Colonic Mucosa	Colon
25	chr1:169822600-169845200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:169825600-169843000	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr1:169825600-169845800	Strong transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:169828200-169843000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:169832200-169843000	Weak transcription	Psoas Muscle	Psoas
32	chr1:169833200-169845600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:169833400-169847000	Strong transcription	Left Ventricle	heart
34	chr1:169833800-169860200	Weak transcription	HMEC	breast
35	chr1:169834200-169843000	Strong transcription	Spleen	Spleen
36	chr1:169834400-169846200	Strong transcription	HSMM	muscle
37	chr1:169834600-169845400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:169834800-169845200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr1:169836800-169843400	Strong transcription	A549	lung
40	chr1:169837000-169843000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:169837400-169848000	Strong transcription	Brain Anterior Caudate	brain
42	chr1:169837800-169845200	Strong transcription	HepG2	liver
43	chr1:169838000-169845000	Strong transcription	Right Ventricle	heart
44	chr1:169838800-169845000	Strong transcription	Brain Cingulate Gyrus	brain
45	chr1:169840000-169846000	Strong transcription	Small Intestine	intestine
46	chr1:169840200-169845200	Strong transcription	Brain Hippocampus Middle	brain
47	chr1:169840400-169843000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:169840400-169846600	Strong transcription	Fetal Stomach	stomach
49	chr1:169840600-169844800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:169841000-169843000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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