Variant report

Variant	rs13083728
Chromosome Location	chr3:52868445-52868446
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52867798..52869834-chr3:52876401..52878497,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11130331	0.82[JPT][hapmap]
rs1134546	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs11918800	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs11922961	0.83[CHB][hapmap];0.82[CHD][hapmap]
rs11922975	0.82[JPT][hapmap]
rs12488303	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12492391	0.95[JPT][hapmap]
rs12496077	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1573815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001735	0.85[ASN][1000 genomes]
rs2071040	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071041	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071042	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2072391	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2239547	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.92[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2240915	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2256332	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2276815	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2276817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2276825	0.91[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336666	0.84[ASN][1000 genomes]
rs2336668	0.95[JPT][hapmap]
rs2336669	0.82[CEU][hapmap];0.82[GIH][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs2535633	0.83[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2564947	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2581780	0.82[CEU][hapmap]
rs2581801	0.81[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs2581810	0.82[CEU][hapmap]
rs2581815	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2878762	0.84[ASN][1000 genomes]
rs35004449	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3733047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3755803	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3821873	0.94[JPT][hapmap]
rs4302374	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4519686	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs4687554	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687559	0.86[ASN][1000 genomes]
rs4687560	0.86[ASN][1000 genomes]
rs4687657	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4687658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4687663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687680	0.95[JPT][hapmap]
rs4687682	0.95[JPT][hapmap]
rs4687687	0.86[JPT][hapmap]
rs6445538	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445541	0.87[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs6445547	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs6445550	0.82[CEU][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap]
rs6768844	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs6769789	0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6790314	0.81[ASW][hapmap];0.89[YRI][hapmap]
rs6792578	0.82[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap]
rs6795646	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs6797399	0.86[ASN][1000 genomes]
rs6798941	0.92[ASN][1000 genomes]
rs6803519	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs7620706	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626551	0.86[JPT][hapmap]
rs7638524	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7648514	0.82[CEU][hapmap]
rs9311485	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs9682464	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810807	0.95[JPT][hapmap]
rs9836499	0.95[JPT][hapmap]
rs9839035	0.86[ASN][1000 genomes]
rs9844736	0.82[CEU][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs9846976	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs9850563	0.95[JPT][hapmap]
rs9860296	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs9865094	0.86[CEU][hapmap]
rs9876403	0.87[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs9880978	0.95[JPT][hapmap]
rs9985365	0.82[JPT][hapmap]

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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription 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	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs13083728	TMEM110	cis	Muscle Skeletal	GTEx
rs13083728	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs13083728	RBM6	cis	cerebellum	SCAN
rs13083728	ITIH4-AS1	cis	Artery Tibial	GTEx
rs13083728	NT5DC2	cis	parietal	SCAN
rs13083728	NEK4	cis	parietal	SCAN
rs13083728	GNL3	cis	parietal	SCAN
rs13083728	ITIH4	cis	lymphoblastoid	seeQTL
rs13083728	ITIH4-AS1	cis	Artery Aorta	GTEx
rs13083728	ITIH4	cis	cerebellum	SCAN
rs13083728	ITIH4-AS1	cis	Whole Blood	GTEx
rs13083728	GLT8D1	cis	lymphoblastoid	seeQTL
rs13083728	GNL3	cis	cerebellum	SCAN
rs13083728	SEMA3G	cis	parietal	SCAN
rs13083728	RFT1	cis	cerebellum	SCAN
rs13083728	MUSTN1	cis	Artery Aorta	GTEx
rs13083728	ITIH4-AS1	cis	lung	GTEx
rs13083728	TMEM110	cis	cerebellum	SCAN
rs13083728	TMEM110	cis	parietal	SCAN
rs13083728	SPCS1	cis	parietal	SCAN
rs13083728	AMT	cis	parietal	SCAN
rs13083728	ITIH4	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
3	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
7	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:52861200-52868800	Weak transcription	Lung	lung
14	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:52865600-52875200	Weak transcription	Dnd41	blood
22	chr3:52865800-52869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
24	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:52866000-52884800	Weak transcription	HMEC	breast
26	chr3:52866200-52868600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
27	chr3:52866200-52869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:52866200-52869200	Weak transcription	Placenta	Placenta
29	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:52866200-52870200	Weak transcription	Gastric	stomach
31	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
33	chr3:52866200-52885200	Weak transcription	NHEK	skin
34	chr3:52866400-52868600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:52866400-52868800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:52866400-52868800	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:52866400-52869800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
39	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:52866600-52868600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:52866600-52868800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:52866600-52868800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:52866600-52868800	Weak transcription	Adipose Nuclei	Adipose
44	chr3:52866600-52868800	Weak transcription	NHDF-Ad	bronchial
45	chr3:52866600-52868800	Weak transcription	NHLF	lung
46	chr3:52866600-52869800	Enhancers	Liver	Liver
47	chr3:52866600-52869800	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
49	chr3:52866600-52879200	Weak transcription	Osteobl	bone
50	chr3:52866800-52868600	Strong transcription	Brain Cingulate Gyrus	brain

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