Variant report

Variant	rs6888170
Chromosome Location	chr5:1641826-1641827
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:1474066..1474782-chr5:1641613..1642314,2	MCF-7	breast:
2	chr5:1479600..1480449-chr5:1641359..1642320,8	K562	blood:
3	chr5:1634031..1636577-chr5:1639531..1641911,4	MCF-7	breast:
4	chr5:1601351..1602385-chr5:1641606..1642321,3	MCF-7	breast:
5	chr5:1380531..1381134-chr5:1641418..1642008,2	K562	blood:
6	chr5:1594724..1595423-chr5:1641483..1642314,2	K562	blood:
7	chr5:1168197..1168876-chr5:1641446..1642294,3	MCF-7	breast:
8	chr5:1637235..1639210-chr5:1639365..1642347,2	K562	blood:
9	chr5:1209132..1210132-chr5:1641419..1642353,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000271119	Chromatin interaction
ENSG00000188002	Chromatin interaction
ENSG00000185986	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11133831	1.00[ASN][1000 genomes]
rs11948870	1.00[ASN][1000 genomes]
rs11951409	1.00[ASN][1000 genomes]
rs11951807	1.00[ASN][1000 genomes]
rs11951980	1.00[ASN][1000 genomes]
rs11952238	1.00[ASN][1000 genomes]
rs11953233	1.00[ASN][1000 genomes]
rs11954077	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11955967	1.00[ASN][1000 genomes]
rs11957991	1.00[ASN][1000 genomes]
rs11958097	1.00[ASN][1000 genomes]
rs2883372	1.00[ASN][1000 genomes]
rs4415117	1.00[ASN][1000 genomes]
rs55864560	1.00[ASN][1000 genomes]
rs55867519	1.00[ASN][1000 genomes]
rs55957581	1.00[ASN][1000 genomes]
rs56185279	1.00[ASN][1000 genomes]
rs57587846	0.85[EUR][1000 genomes]
rs58452381	1.00[ASN][1000 genomes]
rs58687576	1.00[ASN][1000 genomes]
rs59610035	1.00[ASN][1000 genomes]
rs59656356	1.00[ASN][1000 genomes]
rs59806631	1.00[ASN][1000 genomes]
rs61340395	1.00[ASN][1000 genomes]
rs6867199	1.00[ASN][1000 genomes]
rs6869310	1.00[ASN][1000 genomes]
rs6870117	1.00[ASN][1000 genomes]
rs6871261	1.00[ASN][1000 genomes]
rs6872202	1.00[ASN][1000 genomes]
rs6884318	1.00[ASN][1000 genomes]
rs6888910	1.00[ASN][1000 genomes]
rs6889629	1.00[ASN][1000 genomes]
rs6889684	1.00[ASN][1000 genomes]
rs6891099	1.00[ASN][1000 genomes]
rs6898538	1.00[ASN][1000 genomes]
rs72717589	1.00[ASN][1000 genomes]
rs72717593	1.00[ASN][1000 genomes]
rs72717595	1.00[ASN][1000 genomes]
rs72717596	1.00[ASN][1000 genomes]
rs72717598	1.00[ASN][1000 genomes]
rs72717600	1.00[ASN][1000 genomes]
rs72719233	0.81[EUR][1000 genomes]
rs73732121	1.00[ASN][1000 genomes]
rs73732122	1.00[ASN][1000 genomes]
rs73732124	1.00[ASN][1000 genomes]
rs73732134	1.00[ASN][1000 genomes]
rs7705207	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7708447	1.00[ASN][1000 genomes]
rs7716004	1.00[ASN][1000 genomes]
rs7725592	1.00[ASN][1000 genomes]
rs7728463	1.00[ASN][1000 genomes]
rs7728632	1.00[ASN][1000 genomes]
rs7729323	1.00[ASN][1000 genomes]
rs7732756	1.00[ASN][1000 genomes]
rs7736524	1.00[ASN][1000 genomes]
rs7736669	1.00[ASN][1000 genomes]
rs7737033	1.00[ASN][1000 genomes]
rs7737331	1.00[ASN][1000 genomes]

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	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv880788	chr5:1629407-1671200	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv881328	chr5:1637461-1671200	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6888170	SDHAP3	cis	Thyroid	GTEx
rs6888170	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs6888170	SDHAP3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1634600-1645000	Weak transcription	Right Atrium	heart
2	chr5:1634600-1645200	Weak transcription	Gastric	stomach
3	chr5:1640000-1642400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:1640000-1642800	Enhancers	H1 Cell Line	embryonic stem cell
5	chr5:1640400-1642400	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr5:1640400-1643000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:1641200-1642200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:1641400-1642200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr5:1641400-1642200	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr5:1641400-1642200	Enhancers	Fetal Heart	heart
11	chr5:1641400-1643000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:1641600-1642000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
13	chr5:1641600-1642000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:1641600-1642200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:1641600-1642200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr5:1641600-1642200	Enhancers	Duodenum Smooth Muscle	Duodenum
17	chr5:1641600-1642200	Enhancers	Fetal Brain Male	brain
18	chr5:1641600-1642400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr5:1641600-1642400	Enhancers	Hela-S3	cervix
20	chr5:1641600-1643000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:1641800-1642000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:1641800-1642200	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr5:1641800-1642200	Bivalent Enhancer	NH-A	brain

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