Variant report

Variant	rs2613901
Chromosome Location	chr12:74942581-74942582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:74934002..74935915-chr12:74937667..74942932,5	K562	blood:
2	chr12:74933499..74938752-chr12:74938991..74943644,10	K562	blood:
3	chr12:74941646..74944440-chr12:74957364..74960254,2	K562	blood:
4	chr12:74936725..74942637-chr12:74943509..74950364,10	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11180097	0.81[AFR][1000 genomes]
rs12816388	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1389492	0.80[ASN][1000 genomes]
rs1493797	0.90[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1493805	0.81[ASN][1000 genomes]
rs1493806	0.80[ASW][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2605338	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2605374	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2605376	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605377	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613882	0.90[CHB][hapmap]
rs2613887	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2613895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2613900	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2613903	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2641467	0.80[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2641468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641481	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4882641	0.82[ASN][1000 genomes]
rs4882642	0.82[ASN][1000 genomes]
rs597888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs628576	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs647129	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8744	0.92[CEU][hapmap];0.93[CHD][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]

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	nsv1039468	chr12:74080586-75000246	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv899293	chr12:74835107-74995760	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv899295	chr12:74854750-74984992	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv470303	chr12:74880668-74945356	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	n/a
5	nsv899296	chr12:74880668-74974630	Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2613901	ATXN7L3B	cis	parietal	SCAN
rs2613901	KLHDC10	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:74933800-74942800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:74935200-74942600	Weak transcription	Small Intestine	intestine
3	chr12:74935200-74943600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr12:74935200-74945000	Weak transcription	Left Ventricle	heart
5	chr12:74935400-74942600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:74935600-74943200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr12:74935800-74942800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:74936000-74942600	Weak transcription	Fetal Intestine Large	intestine
9	chr12:74936000-74945600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:74936200-74942600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:74936200-74943600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:74936400-74945000	Weak transcription	Fetal Heart	heart
13	chr12:74936800-74942600	Weak transcription	Liver	Liver
14	chr12:74936800-74943000	Weak transcription	Primary T cells from cord blood	blood
15	chr12:74936800-74943200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:74937200-74942600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:74937600-74944400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:74937600-74944600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:74937800-74942800	Weak transcription	HSMM	muscle

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