Variant report

Variant	rs10008927
Chromosome Location	chr4:129729239-129729240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:129472709..129474756-chr4:129728389..129731319,2	MCF-7	breast:
2	chr4:129518963..129527383-chr4:129727996..129735335,14	K562	blood:
3	chr4:129206178..129209105-chr4:129728853..129732712,4	K562	blood:
4	chr4:129207558..129209105-chr4:129728853..129730896,2	K562	blood:

Variant related genes	Relation type
ENSG00000164040	Chromatin interaction
ENSG00000273077	Chromatin interaction
ENSG00000248802	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10032000	0.82[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs12512715	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13120702	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13143771	0.90[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs1648062	0.81[JPT][hapmap]
rs1668289	0.80[JPT][hapmap]
rs1841259	0.87[ASN][1000 genomes]
rs1841260	0.89[ASN][1000 genomes]
rs2016294	0.88[JPT][hapmap]
rs2162126	0.92[CEU][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2217023	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs318500	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs318501	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs318502	0.92[CEU][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs318503	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs318513	0.80[EUR][1000 genomes]
rs318517	0.81[ASN][1000 genomes]
rs318536	0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs318543	0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap]
rs318552	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs318556	0.81[JPT][hapmap]
rs4975265	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4975267	1.00[CEU][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975269	0.82[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4975270	0.88[JPT][hapmap]
rs4975274	0.92[CEU][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62317870	0.87[ASN][1000 genomes]
rs6817004	0.87[ASN][1000 genomes]
rs6834108	0.87[ASN][1000 genomes]
rs6847753	0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs6857659	1.00[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7687562	0.92[CEU][hapmap];0.81[YRI][hapmap];0.97[EUR][1000 genomes];0.95[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	nsv869258	chr4:129191619-130138148	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1020801	chr4:129658178-129778086	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv537248	chr4:129658178-129778086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv822717	chr4:129724785-129739862	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	28 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10008927	SCLT1	cis	cerebellum	SCAN
rs10008927	C4orf33	cis	lymphoblastoid	seeQTL
rs10008927	LOC132321	cis	multi-tissue	Pritchard
rs10008927	PHF17	Cis_1M	lymphoblastoid	RTeQTL
rs10008927	C4orf33	cis	Artery Tibial	GTEx
rs10008927	C4orf33	cis	multi-tissue	Pritchard
rs10008927	C4orf33	Cis_1M	lymphoblastoid	RTeQTL
rs10008927	BCAN	trans	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129723600-129730000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:129723600-129730600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:129724800-129730600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:129725000-129730400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr4:129725200-129730400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:129725400-129730000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr4:129725400-129730200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:129725400-129730200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:129725400-129730400	Weak transcription	Duodenum Mucosa	Duodenum
10	chr4:129725400-129730400	Weak transcription	Stomach Mucosa	stomach
11	chr4:129725600-129730000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:129725600-129730000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr4:129725600-129730000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:129725600-129730000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:129725600-129730200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:129725600-129730200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr4:129725600-129730200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr4:129725600-129730400	Weak transcription	Fetal Intestine Small	intestine
19	chr4:129726200-129730200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:129726200-129730200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:129726200-129730400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:129726200-129730400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr4:129726200-129730800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:129726200-129731200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr4:129726400-129730200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:129726400-129730400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:129726800-129730600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:129727200-129730400	Enhancers	Fetal Heart	heart
29	chr4:129727400-129730400	Weak transcription	Placenta	Placenta
30	chr4:129727400-129730600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr4:129728000-129730200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr4:129728400-129730200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:129728800-129729800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr4:129729000-129729400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr4:129729000-129730200	Enhancers	HUES48 Cell Line	embryonic stem cell

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