Variant report

Variant	rs10865972
Chromosome Location	chr3:52491447-52491448
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52491058-52492925	K562	blood:	n/a	n/a
2	CTCF	chr3:52491340-52491490	GM12873	blood:	n/a	n/a
3	POLR2A	chr3:52491304-52491470	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:52488681..52492997-chr3:52505692..52511376,6	K562	blood:
2	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
3	chr3:52487997..52491865-chr3:52718755..52722667,5	MCF-7	breast:
4	chr3:52487901..52490154-chr3:52491189..52493164,2	K562	blood:
5	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
6	chr3:52490212..52491828-chr3:52494958..52496953,2	K562	blood:

No data

Variant related genes	Relation type
NISCH	TF binding region
TNNC1	TF binding region
ENSG00000163939	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010322	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1011062	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs1011063	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1011064	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs1035002	0.89[EUR][1000 genomes]
rs1035003	0.91[EUR][1000 genomes]
rs1077142	1.00[JPT][hapmap]
rs11707864	1.00[JPT][hapmap]
rs11707931	1.00[JPT][hapmap]
rs11709658	1.00[JPT][hapmap]
rs11711934	1.00[JPT][hapmap]
rs11714402	1.00[JPT][hapmap]
rs11716017	1.00[JPT][hapmap]
rs11718125	1.00[JPT][hapmap]
rs11721286	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs123598	1.00[JPT][hapmap]
rs123602	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs123603	1.00[JPT][hapmap]
rs13059674	1.00[JPT][hapmap]
rs13060192	1.00[JPT][hapmap]
rs13071708	1.00[JPT][hapmap]
rs13074649	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13075370	1.00[JPT][hapmap]
rs13076508	1.00[JPT][hapmap]
rs13076890	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13091360	1.00[JPT][hapmap]
rs13091545	1.00[JPT][hapmap]
rs1541495	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17052058	1.00[JPT][hapmap]
rs17052061	1.00[JPT][hapmap]
rs17052068	1.00[JPT][hapmap]
rs2016575	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs2109558	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109559	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2159607	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2215466	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2335640	1.00[JPT][hapmap]
rs2335928	0.89[EUR][1000 genomes]
rs2335929	0.91[EUR][1000 genomes]
rs2878549	1.00[JPT][hapmap]
rs34261027	0.90[ASN][1000 genomes]
rs34762015	1.00[JPT][hapmap]
rs35860312	1.00[JPT][hapmap]
rs3755810	0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs3774409	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3774410	1.00[JPT][hapmap]
rs3796343	1.00[JPT][hapmap]
rs390802	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs409803	0.82[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs419050	1.00[JPT][hapmap]
rs419604	1.00[JPT][hapmap]
rs419752	1.00[JPT][hapmap]
rs4312651	0.82[CEU][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs4687541	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687543	0.89[EUR][1000 genomes]
rs4687544	0.91[EUR][1000 genomes]
rs4687614	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4687616	0.82[EUR][1000 genomes]
rs4687617	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687618	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4687619	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4687621	0.91[EUR][1000 genomes]
rs498778	1.00[JPT][hapmap]
rs498946	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs613519	0.82[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs634382	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6414568	0.91[EUR][1000 genomes]
rs6445386	1.00[JPT][hapmap]
rs6445484	0.91[EUR][1000 genomes]
rs6445485	0.91[EUR][1000 genomes]
rs6445486	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs6445506	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs676034	1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6763882	1.00[JPT][hapmap]
rs6771558	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6782162	0.91[EUR][1000 genomes]
rs6784615	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6787493	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6796333	1.00[JPT][hapmap]
rs6800707	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6810027	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs728408	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs758800	0.82[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs758803	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs7620015	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs82825	1.00[JPT][hapmap]
rs887514	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs887515	1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs929528	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs929529	0.89[EUR][1000 genomes]
rs9813489	0.90[LWK][hapmap]
rs9813653	1.00[YRI][hapmap]
rs9815559	1.00[YRI][hapmap]
rs9834363	1.00[YRI][hapmap]
rs9834919	0.90[LWK][hapmap]
rs9836166	1.00[YRI][hapmap]
rs9842960	1.00[YRI][hapmap]
rs9843055	1.00[YRI][hapmap]
rs9844178	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs9844183	1.00[JPT][hapmap]
rs9845752	1.00[YRI][hapmap]
rs9846089	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9847332	0.91[EUR][1000 genomes]
rs9850471	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9855470	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9863753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9867823	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv876794	chr3:52485876-52496229	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10865972	STAB1	cis	multi-tissue	Pritchard
rs10865972	ITIH4	cis	multi-tissue	Pritchard
rs10865972	FLJ12442	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52488800-52491800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr3:52490200-52491600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:52490200-52491800	Flanking Active TSS	GM12878-XiMat	blood
4	chr3:52490200-52492600	Flanking Active TSS	HMEC	breast
5	chr3:52490400-52491600	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:52490400-52491600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:52490400-52492000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr3:52490400-52492000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:52490600-52491600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:52490600-52491600	Enhancers	Small Intestine	intestine
11	chr3:52490600-52491800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:52490600-52491800	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr3:52490600-52491800	Enhancers	Spleen	Spleen
14	chr3:52490600-52492200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr3:52490800-52491600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:52490800-52491600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr3:52490800-52491800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:52490800-52491800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:52490800-52491800	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:52490800-52491800	Flanking Active TSS	Fetal Brain Female	brain
21	chr3:52490800-52491800	Enhancers	Gastric	stomach
22	chr3:52490800-52491800	Enhancers	Stomach Mucosa	stomach
23	chr3:52490800-52492000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:52490800-52492200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:52490800-52492400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:52490800-52492400	Weak transcription	Ovary	ovary
27	chr3:52490800-52492400	Weak transcription	Psoas Muscle	Psoas
28	chr3:52490800-52492800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:52490800-52492800	Weak transcription	Aorta	Aorta
30	chr3:52490800-52499200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr3:52491000-52491600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:52491000-52491600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:52491000-52491600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:52491000-52491600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:52491000-52491600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr3:52491000-52491600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:52491000-52491600	Active TSS	Brain Inferior Temporal Lobe	brain
38	chr3:52491000-52491600	Enhancers	Placenta	Placenta
39	chr3:52491000-52491600	Enhancers	Right Ventricle	heart
40	chr3:52491000-52491600	Flanking Active TSS	HSMMtube	muscle
41	chr3:52491000-52491800	Enhancers	Adipose Nuclei	Adipose
42	chr3:52491000-52491800	Enhancers	Left Ventricle	heart
43	chr3:52491000-52491800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:52491000-52491800	Transcr. at gene 5' and 3'	Dnd41	blood
45	chr3:52491000-52491800	Enhancers	K562	blood
46	chr3:52491000-52491800	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr3:52491000-52492000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:52491000-52492000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr3:52491000-52492000	Enhancers	Esophagus	oesophagus
50	chr3:52491000-52492400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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