Variant report

Variant	rs12746471
Chromosome Location	chr1:10475011-10475012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr1:10474901-10476057	A549	lung:	n/a	chr1:10475519-10475531
2	POLR2A	chr1:10474092-10475872	A549	lung:	n/a	n/a
3	ZNF384	chr1:10474966-10475869	K562	blood:	n/a	n/a
4	BCL3	chr1:10475010-10475874	A549	lung:	n/a	n/a
5	SP1	chr1:10474899-10475929	A549	lung:	n/a	chr1:10475519-10475531
6	FOSL2	chr1:10474988-10475863	A549	lung:	n/a	n/a
7	REST	chr1:10475000-10475987	A549	lung:	n/a	n/a
8	POLR2A	chr1:10474839-10475171	A549	lung:	n/a	n/a
9	MAX	chr1:10474646-10475948	A549	lung:	n/a	n/a
10	EP300	chr1:10474983-10476020	A549	lung:	n/a	n/a
11	TCF12	chr1:10474974-10476086	A549	lung:	n/a	chr1:10475573-10475583
12	EP300	chr1:10474928-10476086	A549	lung:	n/a	n/a
13	NR2F2	chr1:10474944-10475936	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10474196..10477325-chr1:10477463..10484153,8	K562	blood:
2	chr1:10457797..10461098-chr1:10474071..10478087,9	K562	blood:
3	chr1:10473791..10476777-chr1:10490511..10492354,2	K562	blood:
4	chr1:10473903..10475499-chr1:10533435..10536154,2	K562	blood:
5	chr1:10474109..10477987-chr1:10478782..10481616,9	K562	blood:
6	chr1:9969356..9971879-chr1:10474323..10477073,2	K562	blood:

No data

Variant related genes	Relation type
PGD	TF binding region
ENSG00000178585	Chromatin interaction
ENSG00000271989	Chromatin interaction
ENSG00000142657	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000175279	Chromatin interaction
ENSG00000251503	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1002076	0.90[ASN][1000 genomes]
rs11121551	0.89[ASN][1000 genomes]
rs11121555	0.89[ASN][1000 genomes]
rs11121557	0.93[ASN][1000 genomes]
rs11121560	0.91[ASN][1000 genomes]
rs11121561	0.97[ASN][1000 genomes]
rs11121563	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11121566	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1138791	0.90[ASN][1000 genomes]
rs11576384	0.96[ASN][1000 genomes]
rs11579365	0.97[ASN][1000 genomes]
rs11585794	0.90[ASN][1000 genomes]
rs11586842	0.87[ASN][1000 genomes]
rs11587309	0.90[ASN][1000 genomes]
rs11587495	0.88[ASN][1000 genomes]
rs11587854	0.90[ASN][1000 genomes]
rs12118323	0.97[ASN][1000 genomes]
rs12128374	0.80[ASN][1000 genomes]
rs12141201	0.90[ASN][1000 genomes]
rs12402723	0.85[EUR][1000 genomes]
rs12409754	0.90[ASN][1000 genomes]
rs1536262	0.93[ASN][1000 genomes]
rs2229687	0.97[ASN][1000 genomes]
rs2236678	0.97[ASN][1000 genomes]
rs34045426	0.95[ASN][1000 genomes]
rs34075302	0.90[ASN][1000 genomes]
rs35716098	0.94[ASN][1000 genomes]
rs35759975	0.97[ASN][1000 genomes]
rs35811280	0.91[ASN][1000 genomes]
rs3737155	0.94[ASN][1000 genomes]
rs3748581	0.92[ASN][1000 genomes]
rs3762286	0.97[ASN][1000 genomes]
rs3762287	0.95[ASN][1000 genomes]
rs3762288	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846216	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4846218	0.87[ASN][1000 genomes]
rs4846219	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4846221	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58014725	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61778404	0.86[ASN][1000 genomes]
rs6541094	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674949	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6682868	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9651117	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers 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 miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv1827009	chr1:10467074-10483456	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv1830329	chr1:10467074-10483456	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
10	esv1831760	chr1:10467074-10483456	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
11	esv1836264	chr1:10473200-10483456	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12746471	PGD	cis	Muscle Skeletal	GTEx
rs12746471	PGD	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10460000-10490200	Weak transcription	Psoas Muscle	Psoas
2	chr1:10460200-10475400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:10460400-10475200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:10460600-10481200	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr1:10460800-10480400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:10460800-10482000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:10460800-10482400	Strong transcription	Fetal Stomach	stomach
8	chr1:10460800-10483400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:10461000-10475200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:10461000-10476800	Weak transcription	Fetal Heart	heart
11	chr1:10461000-10482000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:10461200-10482000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:10461200-10482000	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:10461200-10490000	Weak transcription	Right Atrium	heart
15	chr1:10461400-10475200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:10461400-10483000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:10461400-10483000	Strong transcription	Fetal Intestine Small	intestine
18	chr1:10461400-10483400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr1:10461600-10481800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:10461600-10482800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:10461800-10475200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:10461800-10482000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:10461800-10482000	Strong transcription	Dnd41	blood
24	chr1:10462000-10475200	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr1:10462000-10482000	Strong transcription	Fetal Intestine Large	intestine
26	chr1:10462000-10482200	Strong transcription	Brain Germinal Matrix	brain
27	chr1:10462000-10483000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:10462200-10475200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:10462200-10475400	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:10462200-10475400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:10462200-10481600	Strong transcription	Liver	Liver
32	chr1:10462200-10481600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:10462200-10482000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:10462200-10483200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:10462400-10476000	Strong transcription	Ovary	ovary
36	chr1:10462600-10482000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr1:10462800-10475200	Strong transcription	Placenta	Placenta
38	chr1:10462800-10478200	Strong transcription	Fetal Lung	lung
39	chr1:10462800-10478400	Strong transcription	Brain Angular Gyrus	brain
40	chr1:10462800-10480400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:10462800-10481600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr1:10462800-10481600	Strong transcription	GM12878-XiMat	blood
43	chr1:10462800-10482200	Strong transcription	Thymus	Thymus
44	chr1:10462800-10482600	Strong transcription	Brain Anterior Caudate	brain
45	chr1:10462800-10483400	Strong transcription	Fetal Brain Female	brain
46	chr1:10463000-10475200	Strong transcription	Adipose Nuclei	Adipose
47	chr1:10463000-10476000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:10463000-10478000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr1:10463000-10480800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr1:10463000-10480800	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links