Variant report

Variant	rs3763692
Chromosome Location	chr10:112630201-112630202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:112630029-112630372	HepG2	liver:	n/a	n/a
2	NFATC1	chr10:112630177-112631255	GM12878	blood:	n/a	n/a
3	POLR2A	chr10:112630182-112632933	GM12892	blood:	n/a	n/a
4	POLR2A	chr10:112629899-112634013	GM12891	blood:	n/a	n/a
5	MTA3	chr10:112630172-112633114	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr10:112594090..112596413-chr10:112629473..112632431,2	K562	blood:
2	chr10:112629865..112631826-chr10:112663124..112665657,2	K562	blood:
3	chr10:112581723..112584048-chr10:112629413..112632345,2	K562	blood:
4	chr10:112581444..112587243-chr10:112629842..112633404,6	MCF-7	breast:
5	chr10:112580755..112589346-chr10:112627817..112636075,27	MCF-7	breast:
6	chr10:112630166..112634091-chr10:112649118..112655902,7	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BBIP1-1	chr10:112628648-112631552	NONHSAT016362
2	lnc-BBIP1-1	chr10:112628648-112630662	NONHSAT016363

No data

Variant related genes	Relation type
PDCD4	TF binding region
ENSG00000203867	Chromatin interaction
ENSG00000150593	Chromatin interaction
ENSG00000214413	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10082499	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10787286	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10787291	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10787293	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10885059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885060	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885061	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10885064	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10885071	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10885076	0.83[EUR][1000 genomes]
rs11195361	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11195366	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs11195381	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195387	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11195390	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11195398	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12240685	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12242177	0.81[AFR][1000 genomes]
rs12242928	0.81[AFR][1000 genomes]
rs12258559	0.86[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs12261765	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12776359	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12776861	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146544	0.83[AFR][1000 genomes]
rs34401279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34893229	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35394459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35793075	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35946882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3750619	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4917589	0.86[ASN][1000 genomes]
rs6585026	0.83[EUR][1000 genomes]
rs7089687	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7919142	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv896003	chr10:112579299-112631211	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv896002	chr10:112579299-112638028	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3763692	LOC92482	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112611200-112630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:112617800-112630600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:112618400-112630800	Enhancers	Fetal Thymus	thymus
4	chr10:112621000-112630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr10:112621000-112631000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr10:112621200-112630400	Weak transcription	Gastric	stomach
7	chr10:112621200-112630600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:112621200-112630600	Weak transcription	Brain Substantia Nigra	brain
9	chr10:112623000-112630600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr10:112623400-112631000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:112624000-112630600	Weak transcription	Lung	lung
12	chr10:112625000-112630800	Enhancers	Primary hematopoietic stem cells	blood
13	chr10:112625000-112631000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:112625200-112630800	Enhancers	Thymus	Thymus
15	chr10:112625400-112630400	Weak transcription	Brain Anterior Caudate	brain
16	chr10:112625400-112630600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr10:112625400-112630600	Weak transcription	Brain Hippocampus Middle	brain
18	chr10:112625400-112630600	Enhancers	K562	blood
19	chr10:112625600-112630400	Weak transcription	Fetal Heart	heart
20	chr10:112625600-112630800	Weak transcription	NH-A	brain
21	chr10:112625800-112630400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr10:112625800-112630400	Weak transcription	Colon Smooth Muscle	Colon
23	chr10:112626000-112630400	Weak transcription	Right Atrium	heart
24	chr10:112626000-112630600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr10:112626000-112630600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:112626000-112630800	Enhancers	Primary B cells from peripheral blood	blood
27	chr10:112626000-112630800	Weak transcription	NHLF	lung
28	chr10:112626200-112630400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr10:112626200-112630400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr10:112626200-112630600	Weak transcription	Left Ventricle	heart
31	chr10:112626200-112630600	Weak transcription	Psoas Muscle	Psoas
32	chr10:112626200-112630600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr10:112626200-112630600	Weak transcription	NHEK	skin
34	chr10:112626400-112630400	Weak transcription	Fetal Stomach	stomach
35	chr10:112626400-112630600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr10:112626400-112630800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:112626400-112630800	Weak transcription	HMEC	breast
38	chr10:112626400-112631000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr10:112626800-112630600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr10:112627000-112630600	Weak transcription	Liver	Liver
41	chr10:112627000-112630600	Weak transcription	Esophagus	oesophagus
42	chr10:112627000-112630600	Weak transcription	A549	lung
43	chr10:112627400-112631000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr10:112627600-112630600	Weak transcription	HepG2	liver
45	chr10:112627800-112630400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr10:112627800-112630400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr10:112627800-112630400	Weak transcription	Fetal Intestine Large	intestine
48	chr10:112627800-112630400	Weak transcription	Stomach Mucosa	stomach
49	chr10:112627800-112630800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr10:112627800-112630800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links