Variant report

Variant	rs567884
Chromosome Location	chr5:43123623-43123624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43121173..43123733-chr5:43225214..43227134,2	MCF-7	breast:
2	chr5:43063463..43067998-chr5:43119333..43125586,12	K562	blood:
3	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
4	chr5:43063723..43068505-chr5:43119531..43125230,17	K562	blood:
5	chr5:43120765..43125898-chr5:43482451..43485837,5	K562	blood:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000249888	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10064003	0.90[JPT][hapmap]
rs10522	0.90[JPT][hapmap]
rs10941604	0.86[JPT][hapmap]
rs10941605	0.86[JPT][hapmap]
rs11747714	0.86[JPT][hapmap]
rs12655504	0.80[ASW][hapmap];0.82[CEU][hapmap]
rs12697439	0.90[JPT][hapmap]
rs13169690	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs13170208	0.90[JPT][hapmap]
rs1542369	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs1574407	0.90[JPT][hapmap]
rs160709	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs1618891	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1624415	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1628981	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670796	0.82[CEU][hapmap]
rs1690994	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1690997	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs178415	0.83[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs186324	0.86[JPT][hapmap]
rs2100473	0.86[JPT][hapmap]
rs222060	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2329995	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs2444779	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[YRI][hapmap]
rs2453308	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548334	0.86[JPT][hapmap]
rs2548350	0.81[JPT][hapmap]
rs2548353	0.86[JPT][hapmap]
rs2548356	0.86[JPT][hapmap];0.84[YRI][hapmap]
rs2603644	0.86[JPT][hapmap]
rs2603656	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs2882295	0.86[JPT][hapmap]
rs309909	0.86[JPT][hapmap]
rs309914	0.90[JPT][hapmap]
rs309923	0.86[JPT][hapmap]
rs309924	0.85[JPT][hapmap]
rs309925	0.85[JPT][hapmap]
rs309926	0.85[JPT][hapmap]
rs309927	0.86[JPT][hapmap]
rs309950	0.86[JPT][hapmap]
rs316404	0.83[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs316408	0.83[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs316413	0.83[CEU][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap]
rs316414	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs3909456	0.86[JPT][hapmap]
rs4092293	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs4092294	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs479996	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4866811	0.80[ASW][hapmap];0.83[CEU][hapmap]
rs499436	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs511340	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs512040	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs521649	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541143	0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs544402	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs555276	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs557076	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs574051	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57689195	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579337	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs579363	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61004923	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61121229	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62367758	0.81[AFR][1000 genomes]
rs643307	0.90[JPT][hapmap]
rs6451660	0.90[JPT][hapmap]
rs6451661	0.90[JPT][hapmap]
rs6451662	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs6879130	0.90[JPT][hapmap]
rs6892422	0.86[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724430	0.86[JPT][hapmap]
rs768441	0.90[JPT][hapmap]
rs7715065	0.86[JPT][hapmap]
rs782971	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs782972	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs782976	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782977	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782984	0.93[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782987	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782989	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs782994	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs782996	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903391	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9292862	0.82[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs567884	TTLL7	trans	parietal	SCAN
rs567884	ZNF131	Cis_1M	lymphoblastoid	RTeQTL
rs567884	FYB	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43120800-43123800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr5:43120800-43124000	Active TSS	Psoas Muscle	Psoas
3	chr5:43122000-43123800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:43122200-43123800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr5:43122200-43123800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
6	chr5:43122400-43124000	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr5:43122400-43124200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:43122400-43124200	Transcr. at gene 5' and 3'	K562	blood
9	chr5:43122400-43125000	Transcr. at gene 5' and 3'	Dnd41	blood
10	chr5:43122600-43123800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:43122600-43123800	Enhancers	Liver	Liver
12	chr5:43122600-43124000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:43122600-43124000	Enhancers	Small Intestine	intestine
14	chr5:43122600-43124400	Flanking Active TSS	Fetal Brain Female	brain
15	chr5:43122600-43124400	Enhancers	Stomach Mucosa	stomach
16	chr5:43122600-43126400	Weak transcription	Lung	lung
17	chr5:43122600-43126400	Weak transcription	Spleen	Spleen
18	chr5:43122600-43129200	Weak transcription	Gastric	stomach
19	chr5:43122600-43131200	Weak transcription	Esophagus	oesophagus
20	chr5:43122600-43141600	Weak transcription	Pancreas	Pancrea
21	chr5:43122600-43156200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:43122600-43163400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:43122800-43123800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr5:43122800-43123800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:43122800-43123800	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr5:43122800-43123800	Enhancers	Fetal Kidney	kidney
27	chr5:43122800-43123800	Weak transcription	Fetal Muscle Leg	muscle
28	chr5:43122800-43123800	Weak transcription	Left Ventricle	heart
29	chr5:43122800-43123800	Flanking Active TSS	HepG2	liver
30	chr5:43122800-43124000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
31	chr5:43122800-43124000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:43122800-43124000	Enhancers	Fetal Intestine Small	intestine
33	chr5:43122800-43124200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:43122800-43124400	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr5:43122800-43124400	Transcr. at gene 5' and 3'	Hela-S3	cervix
36	chr5:43122800-43124800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:43122800-43125200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:43122800-43126200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:43122800-43127400	Weak transcription	Ovary	ovary
40	chr5:43122800-43128800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:43122800-43154600	Weak transcription	Aorta	Aorta
42	chr5:43122800-43156400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:43122800-43174200	Weak transcription	Colonic Mucosa	Colon
44	chr5:43123000-43123800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr5:43123000-43123800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr5:43123000-43123800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:43123000-43123800	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr5:43123000-43123800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr5:43123000-43123800	Enhancers	Stomach Smooth Muscle	stomach
50	chr5:43123000-43123800	Enhancers	Monocytes-CD14+_RO01746	blood

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