Variant report

Variant	rs3804772
Chromosome Location	chr3:141634056-141634057
allele	C/T
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	MXI1	chr3:141633390-141634387	IMR90	lung:	n/a	n/a
2	CEBPB	chr3:141633927-141634127	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:141592835..141597303-chr3:141629979..141635181,8	MCF-7	breast:
2	chr3:141594385..141597526-chr3:141631547..141634085,3	K562	blood:
3	chr3:141631967..141634932-chr3:141636891..141639462,2	K562	blood:

Variant related genes	Relation type
ATP1B3	TF binding region
ENSG00000069849	Chromatin interaction
ENSG00000244124	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10755098	0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935439	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10935440	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10935441	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10935442	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935443	0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10935446	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10935447	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11539489	0.84[ASN][1000 genomes]
rs11569259	0.82[EUR][1000 genomes]
rs11569262	0.82[EUR][1000 genomes]
rs11569278	0.82[EUR][1000 genomes]
rs11569281	0.85[EUR][1000 genomes]
rs11569291	0.85[EUR][1000 genomes]
rs11706195	0.86[ASN][1000 genomes]
rs11707100	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11707427	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11710245	0.89[ASN][1000 genomes]
rs11711748	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11713023	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11721024	0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs11844	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486398	0.86[ASN][1000 genomes]
rs12487977	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487983	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490893	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12494971	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12497112	0.90[EUR][1000 genomes]
rs12497443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1560411	0.84[ASN][1000 genomes]
rs16851892	0.88[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2115935	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs2288634	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288635	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2861382	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34071952	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36038301	0.86[ASN][1000 genomes]
rs3762726	0.90[EUR][1000 genomes]
rs3792410	0.89[ASN][1000 genomes]
rs3792411	0.88[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3804773	0.88[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs3828398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683412	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs4683413	0.82[EUR][1000 genomes]
rs4683414	0.82[EUR][1000 genomes]
rs4683638	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4683639	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683640	0.86[ASN][1000 genomes]
rs4683641	0.88[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs4683642	0.86[ASN][1000 genomes]
rs4683643	0.86[ASN][1000 genomes]
rs4683644	0.86[ASN][1000 genomes]
rs4683646	0.89[ASN][1000 genomes]
rs4683647	0.86[ASN][1000 genomes]
rs4683649	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683651	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683652	0.97[EUR][1000 genomes]
rs55945175	0.86[ASN][1000 genomes]
rs59122181	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs745966	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7616903	0.86[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3804772	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:141598000-141642000	Weak transcription	Right Ventricle	heart
3	chr3:141598200-141640200	Weak transcription	Fetal Brain Male	brain
4	chr3:141598200-141640200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:141619400-141641600	Weak transcription	Ovary	ovary
8	chr3:141619600-141640200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:141619600-141644000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:141620400-141641200	Weak transcription	Spleen	Spleen
11	chr3:141620800-141646800	Weak transcription	Gastric	stomach
12	chr3:141621000-141646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
14	chr3:141622000-141645000	Strong transcription	Dnd41	blood
15	chr3:141622000-141647600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:141622400-141647000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:141622600-141644800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
19	chr3:141624200-141635600	Strong transcription	HMEC	breast
20	chr3:141624200-141636600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:141624600-141649200	Weak transcription	Brain Substantia Nigra	brain
22	chr3:141625200-141635400	Strong transcription	NHDF-Ad	bronchial
23	chr3:141625200-141637200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:141625400-141635200	Strong transcription	Primary hematopoietic stem cells	blood
25	chr3:141625600-141634200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:141625600-141647200	Weak transcription	Liver	Liver
27	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr3:141626000-141636600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:141626400-141642200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
31	chr3:141627400-141646600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:141627600-141638200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:141627600-141639200	Weak transcription	Esophagus	oesophagus
34	chr3:141627600-141642200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:141627600-141646400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:141627600-141649200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr3:141627800-141636400	Weak transcription	Colonic Mucosa	Colon
38	chr3:141627800-141652600	Weak transcription	Brain Anterior Caudate	brain
39	chr3:141628200-141640800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:141628600-141635000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:141628600-141636600	Weak transcription	Lung	lung
43	chr3:141628600-141640200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:141628600-141646400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:141628600-141658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:141628800-141640200	Weak transcription	Fetal Brain Female	brain
48	chr3:141628800-141646000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
50	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links