Variant report

Variant	rs4656725
Chromosome Location	chr1:169842527-169842528
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:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10737549	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10737550	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10737551	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs10800479	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800480	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10800481	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10800483	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10800484	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10800485	0.93[EUR][1000 genomes]
rs10800486	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10919245	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10919248	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10919251	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10919257	0.94[ASN][1000 genomes]
rs10919263	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12133843	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1883436	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2056981	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2179396	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281039	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294322	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2294496	0.88[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2420512	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2420514	0.89[EUR][1000 genomes]
rs2491087	0.85[EUR][1000 genomes]
rs2806386	0.83[EUR][1000 genomes]
rs2901179	0.88[ASN][1000 genomes]
rs3753308	0.90[EUR][1000 genomes]
rs3766132	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766134	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766137	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766142	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766144	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3766148	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766151	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3766154	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4376791	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4508080	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4614317	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4615900	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656196	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656197	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4656199	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4656200	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4656721	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656724	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6427220	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6427224	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6427225	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6427226	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6427227	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6427228	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6656965	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6664099	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6668114	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6669794	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6670818	0.90[EUR][1000 genomes]
rs6671752	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6680650	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6680938	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6682137	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6682835	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6683056	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6684481	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6687377	0.92[ASN][1000 genomes]
rs6702969	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs717481	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732185	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519364	0.94[ASN][1000 genomes]
rs7525259	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7530237	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545011	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287097	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4656725	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs4656725	SCYL3	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:169818000-169842800	Strong transcription	Primary B cells from cord blood	blood
13	chr1:169818200-169847800	Strong transcription	Adipose Nuclei	Adipose
14	chr1:169819000-169848200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:169819400-169847000	Strong transcription	Liver	Liver
16	chr1:169820400-169842600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:169820400-169844800	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:169820400-169847200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:169820600-169843000	Strong transcription	Primary T cells from cord blood	blood
20	chr1:169820600-169847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr1:169820600-169847800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:169820600-169848400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr1:169820600-169848600	Strong transcription	Fetal Lung	lung
24	chr1:169821600-169845200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:169822000-169846000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:169822600-169843000	Strong transcription	Colonic Mucosa	Colon
27	chr1:169822600-169845200	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:169825600-169843000	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr1:169825600-169845800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr1:169826800-169848600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:169828200-169843000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr1:169829800-169842800	Strong transcription	Rectal Smooth Muscle	rectum
33	chr1:169831800-169848400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:169832200-169843000	Weak transcription	Psoas Muscle	Psoas
35	chr1:169833200-169845600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:169833400-169847000	Strong transcription	Left Ventricle	heart
37	chr1:169833800-169860200	Weak transcription	HMEC	breast
38	chr1:169834200-169843000	Strong transcription	Spleen	Spleen
39	chr1:169834400-169846200	Strong transcription	HSMM	muscle
40	chr1:169834600-169845400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:169834800-169845200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:169836800-169843400	Strong transcription	A549	lung
43	chr1:169837000-169843000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:169837400-169848000	Strong transcription	Brain Anterior Caudate	brain
45	chr1:169837800-169842800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:169837800-169845200	Strong transcription	HepG2	liver
47	chr1:169838000-169845000	Strong transcription	Right Ventricle	heart
48	chr1:169838800-169845000	Strong transcription	Brain Cingulate Gyrus	brain
49	chr1:169840000-169842600	Weak transcription	NH-A	brain
50	chr1:169840000-169846000	Strong transcription	Small Intestine	intestine

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