Variant report

Variant	rs4647534
Chromosome Location	chr9:97873957-97873958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:97873463-97874108	A549	lung:	n/a	n/a
2	GTF2F1	chr9:97873951-97873969	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:97873561-97875494	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr9:97873943-97874041	HUVEC	blood vessel:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:97870812..97875678-chr9:97877049..97880671,6	MCF-7	breast:
2	chr9:97853610..97855332-chr9:97872385..97874393,2	MCF-7	breast:
3	chr9:97867131..97870318-chr9:97872764..97875795,5	MCF-7	breast:
4	chr9:97767048..97768859-chr9:97873100..97875617,2	MCF-7	breast:
5	chr9:97872125..97874653-chr9:97888365..97890015,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000229065	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10115247	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1045276	0.81[JPT][hapmap]
rs10491560	0.81[JPT][hapmap]
rs10739992	1.00[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10739993	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10761377	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10821451	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10821453	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821454	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10821455	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10993490	0.88[EUR][1000 genomes]
rs13295862	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs171417	0.90[JPT][hapmap]
rs17686583	0.88[EUR][1000 genomes]
rs184818	0.90[JPT][hapmap]
rs1979022	1.00[CEU][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2031599	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap]
rs2166402	1.00[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297596	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2297597	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2404457	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3277	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34045846	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34532504	0.87[EUR][1000 genomes]
rs356666	0.90[JPT][hapmap]
rs356673	0.90[JPT][hapmap]
rs356675	0.90[JPT][hapmap]
rs356677	0.90[JPT][hapmap]
rs356678	0.90[JPT][hapmap]
rs356680	0.90[JPT][hapmap]
rs356684	0.90[JPT][hapmap]
rs356689	0.90[JPT][hapmap]
rs3737142	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3780561	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3780562	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780564	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3780567	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3780568	1.00[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824486	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3844341	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs3852402	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs416792	0.90[JPT][hapmap]
rs4647376	0.88[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap]
rs4647382	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs4647443	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4647459	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4647462	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4647475	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4647528	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4647529	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4647554	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647558	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs4744446	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4744451	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs540412	0.81[JPT][hapmap]
rs565293	0.90[JPT][hapmap]
rs6479601	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7019043	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7023007	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7027204	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs7033633	0.81[JPT][hapmap]
rs7034538	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7850958	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7854570	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7872648	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7874310	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs879492	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs881791	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs944934	0.81[JPT][hapmap]
rs963774	0.96[CEU][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
5	nsv831656	chr9:97831551-97989980	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4647534	LOC57653	cis	cerebellum	SCAN
rs4647534	SYK	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97820600-97875000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr9:97844000-97898400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr9:97846200-97880000	Weak transcription	Primary B cells from cord blood	blood
4	chr9:97847600-97878400	Weak transcription	Dnd41	blood
5	chr9:97855200-97876800	Weak transcription	GM12878-XiMat	blood
6	chr9:97855400-97884800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:97855600-97876400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:97855600-97878600	Weak transcription	Stomach Mucosa	stomach
9	chr9:97858600-97877200	Strong transcription	Fetal Intestine Large	intestine
10	chr9:97858600-97878400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr9:97860000-97875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:97860400-97879000	Strong transcription	Liver	Liver
13	chr9:97861200-97877200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:97861200-97889800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:97862800-97874000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr9:97863200-97875600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:97863400-97874800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:97863600-97883600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:97864000-97877800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:97865200-97876800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:97865200-97877200	Weak transcription	Small Intestine	intestine
22	chr9:97865600-97883600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr9:97865800-97877600	Strong transcription	Fetal Intestine Small	intestine
24	chr9:97866000-97883400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:97866000-97889600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr9:97866200-97889600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:97866400-97875200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr9:97866400-97886600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:97867000-97878800	Weak transcription	Right Atrium	heart
30	chr9:97867800-97877000	Strong transcription	Primary T cells from cord blood	blood
31	chr9:97868600-97889400	Weak transcription	Fetal Heart	heart
32	chr9:97869000-97875400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr9:97869400-97874800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr9:97869400-97875800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:97869400-97876000	Strong transcription	Lung	lung
36	chr9:97869600-97874000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:97869600-97874600	Weak transcription	Fetal Brain Female	brain
38	chr9:97869600-97878800	Weak transcription	Brain Germinal Matrix	brain
39	chr9:97869800-97874200	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr9:97869800-97875400	Strong transcription	A549	lung
41	chr9:97869800-97877200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr9:97869800-97886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr9:97869800-97889800	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr9:97870000-97883400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr9:97870200-97874000	Weak transcription	Colon Smooth Muscle	Colon
46	chr9:97870200-97875200	Strong transcription	Osteobl	bone
47	chr9:97870200-97876600	Weak transcription	Fetal Brain Male	brain
48	chr9:97870400-97878600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr9:97870400-97889600	Weak transcription	Fetal Thymus	thymus
50	chr9:97870600-97889800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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