Variant report

Variant	rs13319651
Chromosome Location	chr3:48599841-48599842
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48595520-48602478	A549	lung:	n/a	n/a
2	USF2	chr3:48598968-48600085	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:48597305-48601913	U87	brain:	n/a	n/a
4	POLR2A	chr3:48598540-48600602	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr3:48597367-48601913	U87	brain:	n/a	n/a
6	POLR2A	chr3:48588992-48602017	U87	brain:	n/a	n/a
7	POLR2A	chr3:48599789-48599949	A549	lung:	n/a	n/a
8	POLR2A	chr3:48595475-48603087	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:48592306-48602182	U87	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48599829-48599879	HL-60	blood:	n/a
2	chr3:48599829-48599879	NB4	blood:	n/a
3	chr3:48599829-48599879	AG04450	lung:	fetal
4	chr3:48599829-48599879	SKMC	muscle:	n/a
5	chr3:48599829-48599879	AG09309	skin:	n/a
6	chr3:48599829-48599879	MCF-7	breast:	n/a
7	chr3:48599829-48599879	Caco-2	colon:	n/a
8	chr3:48599829-48599879	LNCaP	prostate:	n/a
9	chr3:48599829-48599879	NHDF-neo	bronchial:	n/a
10	chr3:48599829-48599879	HCM	heart:	n/a
11	chr3:48599829-48599879	GM12892	blood:	n/a
12	chr3:48599829-48599879	Jurkat	blood:	n/a
13	chr3:48599829-48599879	T-47D	breast:	n/a
14	chr3:48599829-48599879	PFSK-1	brain:	n/a
15	chr3:48599829-48599879	AG04449	skin:	fetal
16	chr3:48599829-48599879	PANC-1	pancreas:	n/a
17	chr3:48599829-48599879	GM06990	blood:	n/a
18	chr3:48599829-48599879	HRCEpiC	kidney:	n/a
19	chr3:48599829-48599879	AG10803	skin:	n/a
20	chr3:48599829-48599879	HCPEpiC	choroid plexus:	n/a
21	chr3:48599829-48599879	AG09319	gingival:	n/a
22	chr3:48599829-48599879	AoSMC	blood vessel:	n/a
23	chr3:48599829-48599879	RPTEC	kidney:	n/a
24	chr3:48599829-48599879	HRPEpiC	eye:	n/a
25	chr3:48599829-48599879	HCF	heart:	n/a
26	chr3:48599829-48599879	MCF10A-Er-Src	breast:	n/a
27	chr3:48599829-48599879	HAEpiC	amniotic membrane:	n/a
28	chr3:48599829-48599879	SAEC	small airway:	n/a
29	chr3:48599829-48599879	A549	lung:	n/a
30	chr3:48599829-48599879	NHBE	bronchial:	n/a
31	chr3:48599829-48599879	HUVEC	blood vessel:	n/a
32	chr3:48599829-48599879	GM12891	blood:	n/a
33	chr3:48599829-48599879	CMK	blood:	n/a
34	chr3:48599829-48599879	ovcar-3	ovarian:	n/a
35	chr3:48599829-48599879	HNPCEpiC	eye:	n/a
36	chr3:48599829-48599879	HepG2	liver:	n/a
37	chr3:48599829-48599879	HEK293	kidney:	embryo
38	chr3:48599829-48599879	GM12878	blood:	n/a
39	chr3:48599829-48599879	HCT-116	colon:	n/a
40	chr3:48599829-48599879	BJ	skin:	n/a
41	chr3:48599829-48599879	SK-N-SH	brain:	n/a
42	chr3:48599829-48599879	NT2-D1	testis:	n/a
43	chr3:48599829-48599879	HPAEpiC	pulmonary alveolar:	n/a
44	chr3:48599829-48599879	SK-N-SH_RA	brain:	n/a
45	chr3:48599829-48599879	K562	blood:	n/a
46	chr3:48599829-48599879	HMEC	breast:	n/a
47	chr3:48599829-48599879	SK-N-MC	brain:	n/a
48	chr3:48599829-48599879	HEEpiC	esophagus:	n/a
49	chr3:48599829-48599879	Hepatocyte	liver:	n/a
50	chr3:48599829-48599879	PrEC	prostate:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr3:48595568..48597473-chr3:48598401..48600580,2	MCF-7	breast:
2	chr3:48592861..48595715-chr3:48598424..48603731,6	K562	blood:
3	chr3:48592800..48598084-chr3:48598125..48603493,9	MCF-7	breast:
4	chr3:48598407..48599969-chr3:48607969..48610789,2	K562	blood:
5	chr3:48598382..48600078-chr3:48601801..48604759,2	K562	blood:
6	chr3:48598893..48601513-chr3:48603815..48606240,3	MCF-7	breast:

No data

Variant related genes	Relation type
PFKFB4	TF binding region
PFKFB4	CpG island
ENSG00000114270	Chromatin interaction
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1003649	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap]
rs10470687	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063312	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13070798	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13094578	0.81[ASN][1000 genomes]
rs13100178	0.81[ASN][1000 genomes]
rs13319635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324142	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2006871	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255532	0.82[CHB][hapmap]
rs2276850	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854394	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2854395	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28563843	0.94[ASN][1000 genomes]
rs28581474	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.86[ASN][1000 genomes]
rs35562294	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35796820	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3755819	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs4075082	0.81[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792156	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6792525	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6806059	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs740787	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7434077	0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs7434107	0.81[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	0.81[ASN][1000 genomes]
rs7631574	0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7640031	0.81[ASN][1000 genomes]
rs7644771	0.81[ASN][1000 genomes]
rs9810549	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.88[TSI][hapmap];0.90[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9810991	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.80[CHB][hapmap];0.85[GIH][hapmap]
rs9816942	0.81[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9830581	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9835902	0.80[CHD][hapmap];0.85[GIH][hapmap]
rs9836462	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9848824	0.94[ASN][1000 genomes]
rs9849280	0.94[ASN][1000 genomes]
rs9850102	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9851743	0.81[ASN][1000 genomes]
rs9851771	0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[ASN][1000 genomes]
rs9864729	0.94[ASN][1000 genomes]
rs9869698	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9871180	0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9871608	0.81[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	0.90[CHD][hapmap];1.00[GIH][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv3811	chr3:48599180-48643809	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48595400-48602000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48596400-48600000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:48596400-48600200	Enhancers	Spleen	Spleen
4	chr3:48596400-48603200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:48596600-48606800	Genic enhancers	A549	lung
6	chr3:48596600-48626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:48597200-48600200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:48597600-48606200	Genic enhancers	HMEC	breast
9	chr3:48598200-48600800	Weak transcription	Hela-S3	cervix
10	chr3:48598600-48600600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:48598600-48601800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:48598600-48603400	Weak transcription	Lung	lung
13	chr3:48598600-48604000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:48598600-48624000	Weak transcription	Aorta	Aorta
15	chr3:48598800-48600800	Weak transcription	Right Atrium	heart
16	chr3:48598800-48601000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:48598800-48604400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:48598800-48604800	Enhancers	Fetal Muscle Trunk	muscle
19	chr3:48598800-48606400	Weak transcription	Colonic Mucosa	Colon
20	chr3:48598800-48609000	Weak transcription	Esophagus	oesophagus
21	chr3:48598800-48615000	Weak transcription	Pancreas	Pancrea
22	chr3:48598800-48617200	Weak transcription	Brain Germinal Matrix	brain
23	chr3:48599000-48600000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:48599000-48600000	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:48599000-48600200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:48599000-48600200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:48599000-48600400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:48599000-48600400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:48599000-48600600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:48599000-48600600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:48599000-48600600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:48599000-48600600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:48599000-48600600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:48599000-48600600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:48599000-48600800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:48599000-48600800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:48599000-48600800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:48599000-48600800	Weak transcription	HUVEC	blood vessel
39	chr3:48599000-48601000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr3:48599000-48601000	Enhancers	Osteobl	bone
41	chr3:48599000-48601200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:48599000-48601200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:48599000-48601200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:48599000-48601200	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:48599000-48601200	Weak transcription	Brain Angular Gyrus	brain
46	chr3:48599000-48601200	Enhancers	HSMM	muscle
47	chr3:48599000-48601400	Enhancers	NH-A	brain
48	chr3:48599000-48601600	Weak transcription	Fetal Intestine Small	intestine
49	chr3:48599000-48602200	Enhancers	HepG2	liver
50	chr3:48599000-48602800	Weak transcription	Adipose Nuclei	Adipose

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