Variant report

Variant	rs13320111
Chromosome Location	chr3:143694570-143694571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143693440..143695168-chr3:143824981..143826507,2	K562	blood:
2	chr3:143694158..143694846-chr3:143996996..143997942,2	MCF-7	breast:
3	chr3:143694108..143696591-chr3:143721286..143722845,2	K562	blood:
4	chr3:143694539..143695086-chr3:144489593..144490285,2	MCF-7	breast:
5	chr3:143694211..143696611-chr3:143698183..143700521,4	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10513239	0.82[CEU][hapmap]
rs11720435	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917772	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13317365	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1604886	0.81[EUR][1000 genomes]
rs2370173	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28627639	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56880774	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6776760	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73000690	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73872672	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7637012	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs964572	0.82[CEU][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823162	0.88[AMR][1000 genomes]
rs9834740	0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9835993	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9847681	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes]
rs9849618	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9860540	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9866992	0.85[AMR][1000 genomes]
rs9870939	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9874033	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9876107	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9879081	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];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:143689000-143695400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
4	chr3:143689200-143695400	Active TSS	K562	blood
5	chr3:143689200-143695800	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr3:143689200-143696200	Active TSS	GM12878-XiMat	blood
7	chr3:143689400-143694800	Active TSS	Brain Anterior Caudate	brain
8	chr3:143689400-143695000	Active TSS	Brain Hippocampus Middle	brain
9	chr3:143689400-143695000	Active TSS	Fetal Brain Male	brain
10	chr3:143689400-143695000	Active TSS	Fetal Intestine Large	intestine
11	chr3:143689400-143695200	Active TSS	NHLF	lung
12	chr3:143689400-143695400	Active TSS	Brain Cingulate Gyrus	brain
13	chr3:143689400-143695400	Active TSS	Right Atrium	heart
14	chr3:143689400-143696200	Active TSS	Brain Angular Gyrus	brain
15	chr3:143689400-143696400	Active TSS	Fetal Brain Female	brain
16	chr3:143689400-143696800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr3:143689400-143697200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:143689600-143694600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:143689600-143695400	Active TSS	HSMM	muscle
20	chr3:143689600-143696800	Active TSS	Ovary	ovary
21	chr3:143689800-143695400	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr3:143689800-143696800	Active TSS	HSMMtube	muscle
23	chr3:143690000-143695600	Active TSS	HMEC	breast
24	chr3:143692000-143695800	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr3:143692200-143695000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:143692600-143707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:143692800-143694600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:143692800-143694800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr3:143692800-143695200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
31	chr3:143693000-143695400	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:143693000-143696200	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr3:143693000-143697800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:143693000-143697800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr3:143693400-143694600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:143693400-143695200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:143693400-143695600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr3:143693400-143697800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr3:143693400-143699400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:143693400-143706800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:143693400-143708400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:143693400-143708400	Weak transcription	Psoas Muscle	Psoas
43	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:143693600-143695000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr3:143693600-143695600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:143693600-143696800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:143693600-143698400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:143693600-143711600	Weak transcription	Left Ventricle	heart
49	chr3:143693800-143694600	Enhancers	Primary hematopoietic stem cells	blood
50	chr3:143693800-143694800	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links