Variant report

Variant	rs7721602
Chromosome Location	chr5:118746010-118746011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:118738573..118740948-chr5:118745923..118747452,2	K562	blood:
2	chr5:118322603..118326136-chr5:118745091..118748767,5	MCF-7	breast:
3	chr5:118745362..118747706-chr5:118750248..118751868,2	K562	blood:
4	chr5:118670103..118672210-chr5:118744741..118746294,2	MCF-7	breast:
5	chr5:118741260..118743708-chr5:118743722..118746283,2	K562	blood:
6	chr5:118735372..118737947-chr5:118745123..118746974,2	MCF-7	breast:
7	chr5:118323688..118325465-chr5:118745878..118747588,2	MCF-7	breast:
8	chr5:118368716..118371473-chr5:118745001..118746920,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10073818	0.80[CHB][hapmap]
rs12656474	0.82[CHB][hapmap]
rs2259347	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs2451804	0.86[EUR][1000 genomes]
rs2451816	0.91[CHB][hapmap]
rs2451818	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2457221	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2546210	0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap]
rs25640	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]
rs257970	0.91[CHB][hapmap];0.81[CHD][hapmap];0.91[MEX][hapmap]
rs257972	0.95[CHB][hapmap]
rs257973	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]
rs257974	0.91[CHB][hapmap]
rs257981	0.85[EUR][1000 genomes]
rs258049	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs258052	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs26180	0.95[CHB][hapmap]
rs26181	0.91[MEX][hapmap]
rs26184	0.91[MEX][hapmap]
rs2636968	0.91[MEX][hapmap]
rs2945327	0.86[CHB][hapmap]
rs32658	0.80[GIH][hapmap]
rs32659	0.91[CHB][hapmap]
rs32662	0.90[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap]
rs32665	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap]
rs408095	0.80[GIH][hapmap]
rs426899	0.85[CEU][hapmap];0.91[MEX][hapmap]
rs455318	0.91[EUR][1000 genomes]
rs455949	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap]
rs461108	0.82[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs462756	0.91[EUR][1000 genomes]
rs463098	0.91[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap]
rs465091	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4895191	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4895371	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4895372	0.91[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6875595	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7720373	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7720678	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv965533	chr5:118738884-118762384	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7721602	HSD17B4	Cis_1M	lymphoblastoid	RTeQTL
rs7721602	SNX24	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118707600-118754600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:118723000-118747600	Weak transcription	Pancreas	Pancrea
3	chr5:118729600-118747400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:118731800-118746600	Weak transcription	Primary T cells from cord blood	blood
5	chr5:118734000-118747400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:118735000-118747000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:118735800-118746200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:118736400-118746600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:118736800-118747400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:118739000-118746200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:118739600-118746800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:118739600-118747000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr5:118739800-118747000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:118741200-118746600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr5:118741400-118746400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr5:118741400-118747000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:118741400-118747400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:118741600-118746800	Weak transcription	K562	blood
19	chr5:118741600-118747000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:118741600-118747400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr5:118742800-118746600	Weak transcription	Primary B cells from cord blood	blood
22	chr5:118744400-118746200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:118744800-118747400	Enhancers	Primary B cells from peripheral blood	blood
24	chr5:118744800-118747400	Enhancers	GM12878-XiMat	blood
25	chr5:118745200-118747400	Enhancers	Fetal Thymus	thymus
26	chr5:118745200-118747600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr5:118745400-118746800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:118745400-118747400	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr5:118745400-118747400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr5:118745400-118747400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:118745600-118746800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr5:118745800-118746600	Weak transcription	Hela-S3	cervix
33	chr5:118746000-118746200	Enhancers	Aorta	Aorta
34	chr5:118746000-118746600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:118746000-118747400	Enhancers	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links