Variant report

Variant	rs2292564
Chromosome Location	chr1:226055595-226055596
allele	A/G
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	chr1:226053730..226055639-chr1:226248303..226251048,2	MCF-7	breast:
2	chr1:226053163..226055606-chr1:226064903..226066639,3	K562	blood:
3	chr1:226054269..226057848-chr1:226069122..226072255,3	K562	blood:
4	chr1:226053727..226055880-chr1:226069290..226070897,2	MCF-7	breast:
5	chr1:225965000..225971731-chr1:226051573..226055609,6	K562	blood:
6	chr1:226054600..226056714-chr1:226056820..226058465,2	MCF-7	breast:
7	chr1:226053217..226056086-chr1:226069002..226071584,2	MCF-7	breast:
8	chr1:226038808..226040415-chr1:226055569..226057247,2	K562	blood:
9	chr1:226054613..226057085-chr1:226059205..226061185,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143742	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12747508	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2292563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2740168	0.85[JPT][hapmap]
rs360076	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs360093	0.87[CEU][hapmap];0.81[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360094	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360096	0.83[CEU][hapmap]
rs360097	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360098	0.91[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs360099	0.83[EUR][1000 genomes]
rs360100	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs360101	0.83[CEU][hapmap]
rs360102	0.83[CEU][hapmap]
rs3820236	0.95[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55936398	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6426090	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515156	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9919303	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2292564	TMEM63A	cis	cerebellum	SCAN
rs2292564	TMEM63A	cis	parietal	SCAN
rs2292564	PARP1	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226026800-226061600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:226033800-226067400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr1:226034000-226056800	Strong transcription	Adipose Nuclei	Adipose
4	chr1:226034000-226063000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr1:226034200-226062800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:226036600-226064600	Weak transcription	Fetal Heart	heart
7	chr1:226036800-226058600	Weak transcription	Brain Germinal Matrix	brain
8	chr1:226036800-226066600	Weak transcription	Fetal Brain Male	brain
9	chr1:226037600-226060600	Strong transcription	Placenta	Placenta
10	chr1:226037800-226065200	Weak transcription	Right Atrium	heart
11	chr1:226038400-226059600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:226038800-226065800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:226039000-226063200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:226039200-226064600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:226039600-226059800	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:226039600-226062200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:226039600-226063000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:226041400-226064600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:226044400-226062800	Strong transcription	Duodenum Mucosa	Duodenum
20	chr1:226044600-226056400	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:226044600-226065800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:226045000-226060800	Strong transcription	Liver	Liver
23	chr1:226046200-226057200	Strong transcription	K562	blood
24	chr1:226046200-226063000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:226046800-226057200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:226046800-226059400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:226047000-226057200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:226047600-226063200	Strong transcription	Left Ventricle	heart
29	chr1:226048000-226055600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:226048000-226060000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:226048400-226062600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:226050200-226068600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:226051600-226056000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:226051800-226055600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:226051800-226066400	Genic enhancers	Primary T cells fromperipheralblood	blood
36	chr1:226052200-226056400	Weak transcription	A549	lung
37	chr1:226052200-226059800	Strong transcription	NHLF	lung
38	chr1:226052600-226057000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:226052600-226057200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:226052600-226064200	Strong transcription	Right Ventricle	heart
41	chr1:226052800-226055800	Genic enhancers	Fetal Thymus	thymus
42	chr1:226052800-226057000	Strong transcription	Colonic Mucosa	Colon
43	chr1:226052800-226057800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:226052800-226059400	Strong transcription	HepG2	liver
45	chr1:226052800-226059800	Strong transcription	Colon Smooth Muscle	Colon
46	chr1:226052800-226060000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:226053000-226055800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr1:226053000-226056800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:226053000-226057000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:226053000-226057200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links