Variant report

Variant	rs865940
Chromosome Location	chr6:44916211-44916212
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1041333	0.81[ASN][1000 genomes]
rs10948185	0.80[AMR][1000 genomes]
rs10948186	0.80[ASN][1000 genomes]
rs10948187	0.84[ASN][1000 genomes]
rs10948188	0.84[ASN][1000 genomes]
rs10948190	0.83[ASN][1000 genomes]
rs10948193	0.83[ASN][1000 genomes]
rs10948194	0.84[ASN][1000 genomes]
rs10948197	0.82[ASN][1000 genomes]
rs1150806	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11967188	0.83[ASN][1000 genomes]
rs12190513	0.84[ASN][1000 genomes]
rs12196818	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12214778	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13196587	0.83[ASN][1000 genomes]
rs13203495	0.83[ASN][1000 genomes]
rs13211229	0.84[ASN][1000 genomes]
rs13216116	0.83[ASN][1000 genomes]
rs1329710	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1329716	0.84[ASN][1000 genomes]
rs1360197	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1521355	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1576382	0.84[ASN][1000 genomes]
rs1590864	0.80[AMR][1000 genomes]
rs17339124	0.83[ASN][1000 genomes]
rs17424547	0.80[ASN][1000 genomes]
rs1831310	0.80[ASN][1000 genomes]
rs1854547	0.84[ASN][1000 genomes]
rs1980265	0.84[ASN][1000 genomes]
rs2396369	0.84[ASN][1000 genomes]
rs2396370	0.84[ASN][1000 genomes]
rs2396371	0.84[ASN][1000 genomes]
rs2396372	0.83[ASN][1000 genomes]
rs35357222	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35813980	0.83[ASN][1000 genomes]
rs3799986	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4711807	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4714830	0.83[ASN][1000 genomes]
rs4714832	0.81[ASN][1000 genomes]
rs472672	0.84[AMR][1000 genomes]
rs494982	0.84[ASN][1000 genomes]
rs500773	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs538801	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55893720	0.83[ASN][1000 genomes]
rs588848	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs608941	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs636845	0.84[ASN][1000 genomes]
rs67001335	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs679713	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6919485	0.84[ASN][1000 genomes]
rs6925017	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7747642	0.82[EUR][1000 genomes]
rs7749865	0.84[ASN][1000 genomes]
rs7775717	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9357464	0.84[ASN][1000 genomes]
rs9463054	0.84[ASN][1000 genomes]
rs9463055	0.81[ASN][1000 genomes]
rs9472409	0.84[ASN][1000 genomes]
rs9472411	0.83[ASN][1000 genomes]
rs9472416	0.83[ASN][1000 genomes]
rs976699	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1033815	chr6:44845514-44938799	Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
6	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
11	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs865940	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44904400-44918800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:44913400-44930000	Weak transcription	Pancreas	Pancrea
3	chr6:44913600-44928600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:44913800-44918200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:44914000-44922800	Weak transcription	HSMM	muscle
6	chr6:44914400-44919200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:44914600-44917200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:44914600-44923000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:44914800-44917000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:44914800-44919200	Weak transcription	Aorta	Aorta
11	chr6:44915000-44917200	Weak transcription	Dnd41	blood
12	chr6:44915200-44917400	Weak transcription	Fetal Heart	heart
13	chr6:44915400-44932800	Weak transcription	Left Ventricle	heart
14	chr6:44916000-44923600	Weak transcription	Stomach Smooth Muscle	stomach

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