Variant report

Variant	rs10915684
Chromosome Location	chr1:224828325-224828326
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224826905..224830184-chr1:224832363..224835221,3	K562	blood:
2	chr1:224805248..224807412-chr1:224827891..224830752,2	K562	blood:
3	chr1:224827571..224830505-chr1:224833018..224834842,2	K562	blood:
4	chr1:224701145..224702114-chr1:224827945..224829840,21	MCF-7	breast:
5	chr1:224821183..224823060-chr1:224827666..224830231,2	K562	blood:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10799277	0.85[EUR][1000 genomes]
rs10799589	0.81[MKK][hapmap]
rs10799590	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10915694	0.81[EUR][1000 genomes]
rs10915696	0.91[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs10915698	1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10915699	0.85[EUR][1000 genomes]
rs10915704	1.00[YRI][hapmap]
rs12092438	0.92[EUR][1000 genomes]
rs12121558	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[YRI][hapmap]
rs12124262	0.95[CEU][hapmap]
rs12130499	0.95[CEU][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12132665	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13374487	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1369847	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1436169	0.91[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1436171	0.86[EUR][1000 genomes]
rs1436172	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs1603917	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1603918	0.87[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169888	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1965777	0.85[EUR][1000 genomes]
rs2050626	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs2050627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2405525	0.85[EUR][1000 genomes]
rs2648746	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2897161	0.80[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2936575	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298732	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298733	0.91[CEU][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298734	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs298735	0.91[CEU][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs298738	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs298739	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2993124	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3012185	0.87[ASW][hapmap];0.91[CEU][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4147293	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs4653402	0.91[CEU][hapmap];0.86[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653404	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653591	0.82[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4653592	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4654060	0.81[MKK][hapmap]
rs56881651	0.86[EUR][1000 genomes]
rs61676104	0.85[EUR][1000 genomes]
rs6667034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686604	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs6686633	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs67817586	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs713098	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7511897	0.86[EUR][1000 genomes]
rs7521396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535296	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537973	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7542431	0.81[EUR][1000 genomes]
rs7542995	0.81[EUR][1000 genomes]
rs7543218	0.91[EUR][1000 genomes]
rs7544312	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7545574	0.91[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs873594	0.86[EUR][1000 genomes]

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	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10915684	DEGS1	cis	cerebellum	SCAN
rs10915684	MARK1	cis	cerebellum	SCAN
rs10915684	RAB3GAP2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224818400-224829400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:224820400-224840000	Weak transcription	Right Atrium	heart
3	chr1:224825200-224828600	Enhancers	Pancreas	Pancrea
4	chr1:224825200-224829400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:224825800-224828800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:224826000-224828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:224826000-224829800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:224826000-224839200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:224826200-224829200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:224826400-224828400	Weak transcription	Dnd41	blood
11	chr1:224826400-224828600	Genic enhancers	NHDF-Ad	bronchial
12	chr1:224826400-224831400	Weak transcription	Thymus	Thymus
13	chr1:224826400-224837800	Weak transcription	NHLF	lung
14	chr1:224827000-224829000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:224827000-224839800	Weak transcription	HSMM	muscle
16	chr1:224827200-224828600	Enhancers	HUES6 Cell Line	embryonic stem cell
17	chr1:224827400-224828600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:224827400-224828800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:224827600-224828400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:224827600-224829000	Enhancers	Fetal Brain Male	brain
21	chr1:224827800-224828400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:224827800-224828400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:224827800-224828600	Genic enhancers	NH-A	brain
24	chr1:224828000-224828600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:224828000-224829000	Enhancers	Gastric	stomach
26	chr1:224828200-224828800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr1:224828200-224829400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links