Variant report

Variant	rs56041446
Chromosome Location	chr1:170041077-170041078
allele	A/G
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	SPI1	chr1:170040205-170041191	GM12878	blood:	n/a	n/a
2	EBF1	chr1:170039811-170041625	GM12878	blood:	n/a	chr1:170040780-170040791
3	POLR2A	chr1:170041005-170041346	MCF10A-Er-Src	breast:	n/a	n/a
4	EBF1	chr1:170040141-170041133	GM12878	blood:	n/a	chr1:170040780-170040791
5	TBP	chr1:170040639-170041159	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170032663..170035514-chr1:170040847..170042460,2	MCF-7	breast:

Variant related genes	Relation type
KIFAP3	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11579254	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11584208	0.92[EUR][1000 genomes]
rs11588736	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1360294	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1572551	0.85[EUR][1000 genomes]
rs16862870	0.92[EUR][1000 genomes]
rs16862874	0.95[EUR][1000 genomes]
rs16862902	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16862943	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1928887	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2150111	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41496844	0.94[EUR][1000 genomes]
rs4656202	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4656730	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4656731	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4656732	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59916635	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61806098	0.92[EUR][1000 genomes]
rs61825319	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61825320	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825343	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61825344	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825346	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825347	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61825348	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61825352	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61825353	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61825354	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61825356	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61825358	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61827261	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73035088	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:170018200-170042400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:170019000-170041400	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:170019000-170042600	Weak transcription	Thymus	Thymus
5	chr1:170019200-170042400	Weak transcription	Fetal Lung	lung
6	chr1:170032800-170042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:170032800-170042600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:170033800-170042400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:170036400-170042200	Weak transcription	NHEK	skin
10	chr1:170036600-170043000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:170036800-170042600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:170037000-170041600	Weak transcription	Right Ventricle	heart
13	chr1:170037000-170042600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr1:170037000-170042800	Weak transcription	Right Atrium	heart
15	chr1:170037000-170043000	Weak transcription	Left Ventricle	heart
16	chr1:170037000-170043200	Weak transcription	Small Intestine	intestine
17	chr1:170037200-170042000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:170037200-170042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:170037200-170042600	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:170037200-170042600	Weak transcription	Fetal Thymus	thymus
21	chr1:170037200-170042600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:170037200-170042600	Weak transcription	HepG2	liver
23	chr1:170037200-170043200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:170037400-170042000	Weak transcription	K562	blood
25	chr1:170037400-170043000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:170037800-170042000	Weak transcription	Adipose Nuclei	Adipose
27	chr1:170037800-170042600	Weak transcription	Fetal Heart	heart
28	chr1:170038000-170043200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:170038400-170041200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:170038400-170041600	Weak transcription	Osteobl	bone
31	chr1:170038400-170042200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:170038600-170041400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:170038600-170041400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:170038600-170042000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:170038600-170042000	Weak transcription	NHLF	lung
36	chr1:170038600-170042600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:170038600-170043000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:170038600-170043000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:170038800-170041400	Enhancers	Dnd41	blood
40	chr1:170038800-170041400	Weak transcription	NHDF-Ad	bronchial
41	chr1:170038800-170041600	Weak transcription	HMEC	breast
42	chr1:170039000-170041200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:170039000-170041200	Weak transcription	Primary T cells from cord blood	blood
44	chr1:170039000-170041200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:170039200-170041400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:170039400-170042600	Weak transcription	Fetal Stomach	stomach
47	chr1:170040000-170042600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr1:170040000-170043000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:170040400-170041600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr1:170040400-170041600	Enhancers	Primary T killer memory cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links