Variant report

Variant	rs56377810
Chromosome Location	chr1:171757657-171757658
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171755451..171759519-chr1:171762178..171766070,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1045456	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489252	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10913683	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913684	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091786	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12565176	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12567851	0.88[EUR][1000 genomes]
rs12730717	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12742601	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12750330	0.88[EUR][1000 genomes]
rs12753043	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17596025	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17596081	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17649609	0.98[EUR][1000 genomes]
rs17650310	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650340	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17657363	0.91[EUR][1000 genomes]
rs1801898	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2143369	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2181216	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2223602	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2232807	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232819	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2232824	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2232825	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs236894	0.82[EUR][1000 genomes]
rs236897	0.87[EUR][1000 genomes]
rs236898	0.87[EUR][1000 genomes]
rs236899	0.86[EUR][1000 genomes]
rs236900	0.86[EUR][1000 genomes]
rs34320898	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34627492	0.89[EUR][1000 genomes]
rs35249022	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35400839	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35631282	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35674909	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35882887	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35930163	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36080557	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3891278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732843	0.91[EUR][1000 genomes]
rs56365362	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61807979	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6656852	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674364	0.98[EUR][1000 genomes]
rs6675708	0.98[EUR][1000 genomes]
rs6681322	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6689125	0.95[EUR][1000 genomes]
rs6695933	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7522582	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7536142	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv872545	chr1:171735198-171805448	Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv518222	chr1:171753039-171763549	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56377810	KIAA0859	Cis_1M	lymphoblastoid	RTeQTL
rs56377810	DNM3	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171751600-171770800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:171752000-171773600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:171752200-171759200	Weak transcription	Fetal Heart	heart
4	chr1:171752200-171762200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:171752200-171766600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:171752200-171767400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:171752200-171768200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr1:171752400-171766600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:171752400-171767200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:171752600-171760000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:171752600-171767000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr1:171752600-171767000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:171752600-171767400	Strong transcription	Primary B cells from cord blood	blood
14	chr1:171752600-171767400	Strong transcription	A549	lung
15	chr1:171752600-171767800	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:171752600-171767800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:171752800-171757800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:171752800-171761800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:171752800-171762600	Strong transcription	Fetal Stomach	stomach
20	chr1:171752800-171765800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:171752800-171766600	Strong transcription	Placenta	Placenta
22	chr1:171752800-171767200	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr1:171752800-171770200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr1:171753000-171757800	Strong transcription	Brain Cingulate Gyrus	brain
25	chr1:171753000-171762000	Strong transcription	Colonic Mucosa	Colon
26	chr1:171753000-171763400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:171753000-171766200	Strong transcription	Brain Substantia Nigra	brain
28	chr1:171753000-171766800	Strong transcription	H9 Cell Line	embryonic stem cell
29	chr1:171753000-171766800	Strong transcription	Brain Hippocampus Middle	brain
30	chr1:171753000-171767200	Strong transcription	Fetal Lung	lung
31	chr1:171753000-171767600	Strong transcription	Fetal Intestine Large	intestine
32	chr1:171753600-171760400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:171753600-171767800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:171753800-171758200	Strong transcription	NH-A	brain
35	chr1:171754000-171767200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:171754000-171767600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:171754000-171767800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:171754000-171767800	Strong transcription	Thymus	Thymus
39	chr1:171754200-171758000	Strong transcription	Colon Smooth Muscle	Colon
40	chr1:171754200-171761600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:171754200-171762400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:171754200-171763000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:171754200-171766600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:171754200-171767000	Strong transcription	Brain Angular Gyrus	brain
45	chr1:171754200-171767800	Strong transcription	Brain Anterior Caudate	brain
46	chr1:171754200-171767800	Strong transcription	Brain Germinal Matrix	brain
47	chr1:171754200-171768000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:171754200-171768000	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:171754200-171769600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:171754200-171770200	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links