Variant report

Variant	rs793443
Chromosome Location	chr3:99573547-99573548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:99573466-99573606	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:99571804-99576711	HepG2	liver:	n/a	n/a
3	MBD4	chr3:99573231-99574260	HepG2	liver:	n/a	n/a
4	CTCF	chr3:99573400-99573550	GM12866	blood:	n/a	n/a
5	POLR2A	chr3:99572382-99573719	HepG2	liver:	n/a	n/a
6	MAFK	chr3:99573496-99573801	HepG2	liver:	n/a	n/a
7	MAFK	chr3:99573465-99573737	HepG2	liver:	n/a	n/a
8	CTCF	chr3:99573440-99573590	HCPEpiC	choroid plexus:	n/a	n/a
9	POLR2A	chr3:99573355-99573754	SK-N-SH	brain:	n/a	n/a
10	CTCF	chr3:99573492-99573558	K562	blood:	n/a	n/a
11	POLR2A	chr3:99573456-99573711	ProgFib	skin:	n/a	n/a
12	CTCF	chr3:99573420-99573570	GM12864	blood:	n/a	n/a
13	CTCF	chr3:99573460-99573610	HRE	kidney:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99565608..99567725-chr3:99572661..99574736,2	K562	blood:
2	chr3:99572189..99574977-chr3:99579717..99581274,2	MCF-7	breast:
3	chr3:99570458..99572667-chr3:99573247..99575806,2	MCF-7	breast:
4	chr3:99564230..99568192-chr3:99570896..99574736,4	K562	blood:
5	chr3:99572300..99574095-chr3:99587756..99590558,2	MCF-7	breast:

No data

Variant related genes	Relation type
FILIP1L	TF binding region
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1287284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1384062	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1610509	0.88[JPT][hapmap]
rs16841874	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs1718235	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2638948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35422475	0.82[AMR][1000 genomes]
rs4577503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4928230	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4928235	0.81[AMR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs58704213	0.81[ASN][1000 genomes]
rs6440967	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs6806323	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs7650727	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs766778	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs792831	0.88[JPT][hapmap]
rs792835	0.88[JPT][hapmap]
rs792836	0.88[JPT][hapmap]
rs792837	0.88[JPT][hapmap]
rs793437	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793440	0.82[TSI][hapmap]
rs793446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793476	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793503	0.82[TSI][hapmap]
rs796976	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs902159	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs923472	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]

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	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs793443	FILIP1L	cis	parietal	SCAN
rs793443	OR5H6	cis	cerebellum	SCAN
rs793443	SENP7	cis	parietal	SCAN
rs793443	C3orf26	cis	multi-tissue	Pritchard
rs793443	EPHX1	trans	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99538200-99584600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99557000-99573600	Weak transcription	Small Intestine	intestine
4	chr3:99559000-99578000	Weak transcription	HMEC	breast
5	chr3:99562200-99578000	Weak transcription	NHEK	skin
6	chr3:99562600-99578200	Weak transcription	Fetal Kidney	kidney
7	chr3:99562800-99580200	Weak transcription	Gastric	stomach
8	chr3:99563000-99575000	Weak transcription	Placenta	Placenta
9	chr3:99563000-99577600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:99563200-99574800	Weak transcription	Psoas Muscle	Psoas
11	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:99563800-99574800	Weak transcription	Pancreas	Pancrea
13	chr3:99564200-99577600	Weak transcription	Primary B cells from cord blood	blood
14	chr3:99565200-99585000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr3:99565400-99577600	Weak transcription	Fetal Heart	heart
16	chr3:99565600-99573600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:99565600-99573600	Weak transcription	Fetal Lung	lung
18	chr3:99565600-99574800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:99565600-99574800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:99565600-99584800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:99565600-99589400	Weak transcription	K562	blood
22	chr3:99566000-99578400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:99567600-99573600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:99567600-99576200	Weak transcription	Stomach Mucosa	stomach
25	chr3:99567800-99581600	Weak transcription	Spleen	Spleen
26	chr3:99568000-99578600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr3:99568000-99580000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:99568400-99575000	Weak transcription	GM12878-XiMat	blood
29	chr3:99568400-99576000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:99568600-99577600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:99568800-99574800	Weak transcription	NHDF-Ad	bronchial
32	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
33	chr3:99569800-99575000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:99569800-99579200	Weak transcription	Right Ventricle	heart
35	chr3:99569800-99579400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:99569800-99580200	Weak transcription	Lung	lung
37	chr3:99570000-99575200	Weak transcription	NHLF	lung
38	chr3:99570000-99575600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:99570000-99576000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:99570000-99576200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:99570000-99577600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:99570200-99574800	Weak transcription	HSMM	muscle
43	chr3:99570400-99573600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:99570400-99573800	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr3:99570400-99574800	Weak transcription	Fetal Stomach	stomach
46	chr3:99570400-99579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:99570400-99579200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:99570600-99581600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:99570800-99577400	Weak transcription	Fetal Intestine Large	intestine
50	chr3:99571000-99574400	Weak transcription	HUVEC	blood vessel

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