Variant report

Variant	rs1259405
Chromosome Location	chr12:31712513-31712514
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31711892..31714332-chr12:31715777..31718020,2	K562	blood:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1012154	0.82[CEU][hapmap]
rs11051456	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150942	0.91[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150943	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150945	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150950	0.88[AFR][1000 genomes]
rs1150953	0.90[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1150954	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150955	0.95[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150963	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259233	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259235	0.91[CEU][hapmap]
rs1259241	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259352	0.81[EUR][1000 genomes]
rs1259353	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259354	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259356	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259359	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259386	0.98[ASN][1000 genomes]
rs1259389	0.88[ASN][1000 genomes]
rs1259395	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1259409	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259422	1.00[AFR][1000 genomes]
rs1259426	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259430	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1259435	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259437	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259438	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259441	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1262390	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1271663	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1272773	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1542536	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1677154	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1677186	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677187	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677189	0.82[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1677217	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1716194	0.88[ASN][1000 genomes]
rs1716210	0.88[AMR][1000 genomes]
rs1716216	0.90[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2061761	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2374190	0.90[CEU][hapmap]
rs2568885	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568887	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2604052	0.98[ASN][1000 genomes]
rs2617178	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617191	0.90[CEU][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2617200	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2682671	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682674	0.86[ASN][1000 genomes]
rs2682677	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682679	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682680	0.83[ASN][1000 genomes]
rs2682686	0.81[EUR][1000 genomes]
rs2682695	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4312145	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs708212	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs708215	0.81[AMR][1000 genomes]
rs708217	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs792871	0.90[CEU][hapmap]
rs792875	0.81[AMR][1000 genomes]
rs793148	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793149	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793150	1.00[CEU][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793158	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793161	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs793171	0.91[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs793173	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793174	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793175	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793176	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs793177	0.90[CEU][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793186	1.00[CEU][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs793191	0.90[CEU][hapmap]
rs899159	0.98[ASN][1000 genomes]
rs976874	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv983241	chr12:31701617-31712747	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31689000-31713000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr12:31696200-31722400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:31709200-31727600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:31709400-31713000	Weak transcription	Aorta	Aorta
5	chr12:31709400-31722600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:31709600-31713200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:31709800-31713200	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:31710000-31714600	Weak transcription	A549	lung
9	chr12:31710200-31723800	Weak transcription	Pancreas	Pancrea
10	chr12:31710800-31713400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:31711000-31713400	Weak transcription	Fetal Intestine Small	intestine
12	chr12:31711000-31713600	Weak transcription	Ovary	ovary
13	chr12:31711000-31727400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr12:31711400-31712800	Weak transcription	HepG2	liver
15	chr12:31711400-31713000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:31712000-31713000	Weak transcription	GM12878-XiMat	blood
17	chr12:31712200-31713200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:31712200-31713200	Enhancers	Osteobl	bone
19	chr12:31712200-31713400	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr12:31712200-31721000	Weak transcription	Primary B cells from cord blood	blood
21	chr12:31712200-31723600	Weak transcription	NH-A	brain

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