Variant report

Variant	rs2817198
Chromosome Location	chr6:24575094-24575095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24574532..24577193-chr6:24720841..24722364,2	MCF-7	breast:
2	chr6:24570345..24573148-chr6:24573437..24575149,2	K562	blood:
3	chr6:24570050..24571845-chr6:24573649..24576621,2	K562	blood:
4	chr6:24573525..24576686-chr6:24578975..24580891,3	K562	blood:
5	chr6:24574766..24576618-chr6:24701897..24704252,2	K562	blood:

Variant related genes	Relation type
ENSG00000272345	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs2076313	0.82[JPT][hapmap]
rs2243831	0.82[JPT][hapmap]
rs2744542	0.82[JPT][hapmap]
rs2744543	0.82[JPT][hapmap]
rs2744556	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2744559	0.83[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs2744562	0.87[AFR][1000 genomes]
rs2760155	0.91[AFR][1000 genomes]
rs2760156	0.91[AFR][1000 genomes]
rs2760159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2760165	0.82[JPT][hapmap]
rs2760172	1.00[JPT][hapmap]
rs2760173	1.00[JPT][hapmap]
rs2760174	1.00[JPT][hapmap]
rs2760175	1.00[JPT][hapmap]
rs2760179	1.00[JPT][hapmap]
rs2817250	0.82[JPT][hapmap]
rs2817251	1.00[JPT][hapmap]
rs2817253	0.82[JPT][hapmap]
rs2817255	0.82[JPT][hapmap]
rs72834991	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9467220	0.82[JPT][hapmap]
rs9467231	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1020653	chr6:24557870-24638244	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2817198	CDKAL1	cis	cerebellum	SCAN
rs2817198	HIST1H2BA	cis	cerebellum	SCAN
rs2817198	HIST1H4L	cis	parietal	SCAN
rs2817198	BTN1A1	cis	cerebellum	SCAN
rs2817198	GMNN	cis	parietal	SCAN
rs2817198	HIST1H4D	cis	parietal	SCAN
rs2817198	HIST1H3B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24496200-24583000	Weak transcription	Hela-S3	cervix
2	chr6:24535200-24591200	Weak transcription	Fetal Brain Male	brain
3	chr6:24535600-24583400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:24539200-24583200	Weak transcription	Fetal Intestine Small	intestine
5	chr6:24548400-24583400	Weak transcription	A549	lung
6	chr6:24559600-24577600	Weak transcription	Pancreas	Pancrea
7	chr6:24562400-24583400	Weak transcription	Right Atrium	heart
8	chr6:24564400-24583400	Weak transcription	Brain Angular Gyrus	brain
9	chr6:24564400-24583400	Weak transcription	Brain Anterior Caudate	brain
10	chr6:24569200-24576600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:24570200-24583400	Weak transcription	Brain Germinal Matrix	brain
12	chr6:24570200-24583600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:24572200-24584200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:24572800-24576600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:24573600-24584000	Weak transcription	Fetal Brain Female	brain
16	chr6:24575000-24575200	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr6:24575000-24575400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:24575000-24575400	Flanking Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr6:24575000-24575600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr6:24575000-24575600	Enhancers	Primary B cells from cord blood	blood
21	chr6:24575000-24575600	Enhancers	GM12878-XiMat	blood
22	chr6:24575000-24575800	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:24575000-24576000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links