Variant report

Variant	rs2844662
Chromosome Location	chr6:30817879-30817880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr6:30817580-30818077	SK-N-SH	brain:	n/a	n/a
2	KAP1	chr6:30817543-30818341	K562	blood:	n/a	n/a
3	PBX3	chr6:30817530-30818059	SK-N-SH	brain:	n/a	n/a
4	TCF12	chr6:30817483-30818055	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr6:30817529-30818199	SK-N-SH	brain:	n/a	n/a
6	SETDB1	chr6:30817863-30818262	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30816135..30818662-chr6:30876790..30878789,2	K562	blood:
2	chr6:30814424..30817937-chr6:30849019..30852528,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237923	TF binding region
ENSG00000204580	Chromatin interaction
ENSG00000213780	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1264297	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264298	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264299	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264300	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264301	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264302	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264303	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264305	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1264307	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264309	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264317	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264320	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264332	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1264342	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17189763	0.86[EUR][1000 genomes]
rs2074506	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240804	0.87[EUR][1000 genomes]
rs2249459	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2252760	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252856	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252863	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394856	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517449	0.90[EUR][1000 genomes]
rs2517457	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2517461	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517462	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517463	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517466	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2517468	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2517573	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517577	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2517582	0.85[EUR][1000 genomes]
rs2532920	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532921	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2532927	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532928	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2532929	0.82[EUR][1000 genomes]
rs2532930	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532933	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532935	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2532936	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532937	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532938	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532939	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532940	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532942	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2532943	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2535325	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535326	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2535327	0.88[EUR][1000 genomes]
rs2535329	0.88[EUR][1000 genomes]
rs2535330	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535331	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535335	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535336	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535337	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535339	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844652	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2844654	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2844655	0.88[EUR][1000 genomes]
rs2844658	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844663	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844664	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2844698	0.83[ASN][1000 genomes]
rs2844699	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2844702	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130657	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs753726	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7738138	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7756286	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs887381	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9262288	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262289	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262290	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262291	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262292	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262293	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9262294	0.91[EUR][1000 genomes];0.94[ASN][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	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2844662	GRM4	cis	parietal	SCAN
rs2844662	VARSL	cis	multi-tissue	Pritchard
rs2844662	HIST1H2AH	cis	cerebellum	SCAN
rs2844662	DDR1	cis	lymphoblastoid	seeQTL
rs2844662	LTB	cis	lymphoblastoid	seeQTL
rs2844662	HLA-H	cis	multi-tissue	Pritchard
rs2844662	GTF2H4///VARS2	Cis_1M	lymphoblastoid	RTeQTL
rs2844662	HLA-C	cis	multi-tissue	Pritchard

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30812400-30822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:30812600-30820600	Weak transcription	Right Atrium	heart
3	chr6:30816200-30822200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:30816200-30824600	Weak transcription	Fetal Kidney	kidney
5	chr6:30816600-30818000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:30816600-30819400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:30817200-30818000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:30817200-30818000	Enhancers	Fetal Lung	lung
9	chr6:30817400-30818000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
10	chr6:30817400-30820600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
11	chr6:30817600-30818000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
12	chr6:30817600-30818000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links