Variant report

Variant	rs625507
Chromosome Location	chr1:47133060-47133061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:47132948-47134691	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:47132830-47134920	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47132421..47133961-chr1:47797739..47800236,2	K562	blood:
2	chr1:47131887..47139340-chr1:47181784..47186573,11	K562	blood:
3	chr1:47132021..47134292-chr1:47182751..47186267,3	MCF-7	breast:
4	chr1:47124121..47126688-chr1:47131484..47133286,2	K562	blood:
5	chr1:47130612..47137538-chr1:47138503..47143012,9	K562	blood:
6	chr1:47131372..47133587-chr1:47151853..47154733,2	MCF-7	breast:
7	chr1:47077660..47081751-chr1:47132686..47135354,3	MCF-7	breast:

No data

Variant related genes	Relation type
TEX38	TF binding region
ENSG00000233647	TF binding region
ATPAF1	TF binding region
ENSG00000142961	Chromatin interaction
ENSG00000162368	Chromatin interaction
ENSG00000228237	Chromatin interaction
ENSG00000123472	Chromatin interaction
ENSG00000159658	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10158678	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10159351	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1025806	0.93[EUR][1000 genomes]
rs1048351	0.92[EUR][1000 genomes]
rs1048380	0.90[EUR][1000 genomes]
rs1075982	0.92[EUR][1000 genomes]
rs10789492	0.82[EUR][1000 genomes]
rs10789493	0.82[EUR][1000 genomes]
rs10890411	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10890415	0.80[EUR][1000 genomes]
rs10890416	0.84[EUR][1000 genomes]
rs11211338	0.94[EUR][1000 genomes]
rs11211341	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211344	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211346	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211349	0.80[EUR][1000 genomes]
rs11211354	0.82[EUR][1000 genomes]
rs1139758	0.91[EUR][1000 genomes]
rs1150064	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150068	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11801316	0.94[EUR][1000 genomes]
rs11801419	0.88[EUR][1000 genomes]
rs11804665	0.91[EUR][1000 genomes]
rs12047537	0.92[EUR][1000 genomes]
rs12078635	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12082387	0.88[EUR][1000 genomes]
rs12094663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258000	0.82[EUR][1000 genomes]
rs1258002	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1258052	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1258053	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258054	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258056	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1258059	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13417	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1440486	0.93[EUR][1000 genomes]
rs1440489	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1440491	0.81[EUR][1000 genomes]
rs17102352	0.91[EUR][1000 genomes]
rs17102355	0.91[EUR][1000 genomes]
rs17102473	0.90[EUR][1000 genomes]
rs1745377	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1933933	0.92[EUR][1000 genomes]
rs1962900	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1971519	0.82[EUR][1000 genomes]
rs2083486	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119301	0.93[EUR][1000 genomes]
rs2218189	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241862	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289446	0.92[EUR][1000 genomes]
rs2289447	0.90[EUR][1000 genomes]
rs2304745	0.93[EUR][1000 genomes]
rs2405026	0.93[EUR][1000 genomes]
rs2405030	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34932727	0.92[EUR][1000 genomes]
rs3737731	0.93[EUR][1000 genomes]
rs3766211	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766212	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766214	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3766215	0.93[EUR][1000 genomes]
rs3766217	0.93[EUR][1000 genomes]
rs3766219	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3766224	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4272563	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4274009	0.91[EUR][1000 genomes]
rs4301586	0.94[EUR][1000 genomes]
rs4412540	0.80[EUR][1000 genomes]
rs4443838	0.92[EUR][1000 genomes]
rs55914029	0.90[EUR][1000 genomes]
rs56319728	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58185502	0.90[EUR][1000 genomes]
rs585257	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs594118	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs595813	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59881815	0.92[EUR][1000 genomes]
rs60173509	0.92[EUR][1000 genomes]
rs60675294	0.93[EUR][1000 genomes]
rs611468	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614486	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61782563	0.93[EUR][1000 genomes]
rs61782564	0.93[EUR][1000 genomes]
rs61782568	0.93[EUR][1000 genomes]
rs61782590	0.81[EUR][1000 genomes]
rs61784001	0.92[EUR][1000 genomes]
rs61784002	0.92[EUR][1000 genomes]
rs61784003	0.94[EUR][1000 genomes]
rs618554	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs618878	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs620431	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs620913	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625590	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs637760	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638845	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6429607	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6429608	0.86[EUR][1000 genomes]
rs6429609	0.89[EUR][1000 genomes]
rs6429610	0.83[EUR][1000 genomes]
rs647999	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666405	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6667885	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6669393	0.91[EUR][1000 genomes]
rs6670495	0.83[EUR][1000 genomes]
rs6671005	0.93[EUR][1000 genomes]
rs6671124	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6688195	0.93[EUR][1000 genomes]
rs6690193	0.81[EUR][1000 genomes]
rs723334	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs723690	0.82[EUR][1000 genomes]
rs732539	0.94[EUR][1000 genomes]
rs7354865	0.94[EUR][1000 genomes]
rs7354894	0.81[EUR][1000 genomes]
rs7412469	0.93[EUR][1000 genomes]
rs744096	0.92[EUR][1000 genomes]
rs7519866	0.86[EUR][1000 genomes]
rs7532601	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7534179	0.82[EUR][1000 genomes]
rs7541868	0.94[EUR][1000 genomes]
rs7553243	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8851	0.81[EUR][1000 genomes]
rs946320	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1013048	chr1:47132831-47377364	Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv534955	chr1:47132831-47377364	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs625507	ATPAF1	Cis_1M	lymphoblastoid	RTeQTL
rs625507	KIAA0494	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47131600-47133400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:47131600-47133400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr1:47131800-47133400	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr1:47132000-47133200	Enhancers	Fetal Heart	heart
5	chr1:47132000-47133200	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:47132000-47133400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:47132000-47133400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr1:47132000-47133600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr1:47132200-47133200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:47132200-47133400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:47132200-47133400	Flanking Active TSS	Fetal Brain Male	brain
12	chr1:47132200-47133400	Flanking Active TSS	Rectal Smooth Muscle	rectum
13	chr1:47132200-47133400	Flanking Active TSS	GM12878-XiMat	blood
14	chr1:47132200-47133600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
15	chr1:47132400-47133200	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr1:47132400-47133400	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr1:47132400-47133400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr1:47132400-47133400	Flanking Active TSS	Brain Hippocampus Middle	brain
19	chr1:47132400-47133400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:47132400-47133400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:47132400-47133400	Enhancers	Small Intestine	intestine
22	chr1:47132400-47133400	Flanking Active TSS	Thymus	Thymus
23	chr1:47132400-47133600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:47132400-47133600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:47132400-47133600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:47132400-47133600	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr1:47132400-47133600	Flanking Active TSS	Fetal Lung	lung
28	chr1:47132400-47133600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr1:47132600-47133200	Flanking Active TSS	Brain Cingulate Gyrus	brain
30	chr1:47132600-47133200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr1:47132600-47133200	Flanking Active TSS	HepG2	liver
32	chr1:47132600-47133400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:47132600-47133400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:47132600-47133400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr1:47132600-47133400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:47132600-47133400	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr1:47132600-47133400	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr1:47132600-47133400	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr1:47132600-47133400	Flanking Active TSS	Colon Smooth Muscle	Colon
40	chr1:47132600-47133400	Flanking Active TSS	Fetal Brain Female	brain
41	chr1:47132600-47133400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr1:47132600-47133400	Flanking Active TSS	Dnd41	blood
43	chr1:47132600-47133400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr1:47132600-47133400	Flanking Active TSS	NHLF	lung
45	chr1:47132600-47133600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:47132600-47133600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr1:47132600-47133600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr1:47132600-47133600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr1:47132600-47133600	Active TSS	Right Atrium	heart
50	chr1:47132600-47133800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links