Variant report

Variant	rs1259430
Chromosome Location	chr12:31673875-31673876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31633164..31634718-chr12:31672304..31674554,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1012154	0.80[CEU][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150942	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1150943	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150945	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150953	0.89[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1150954	0.84[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1150955	0.90[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1150963	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1259233	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1259235	0.90[CEU][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259241	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1259353	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1259354	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1259355	0.83[ASN][1000 genomes]
rs1259356	0.84[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1259359	0.84[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1259400	0.87[EUR][1000 genomes]
rs1259401	0.84[EUR][1000 genomes]
rs1259405	0.85[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1259409	0.87[CEU][hapmap]
rs1259422	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1259423	0.84[EUR][1000 genomes]
rs1259427	0.85[EUR][1000 genomes]
rs1259428	0.83[ASN][1000 genomes]
rs1259432	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1259435	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259437	0.85[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259438	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1259441	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1262390	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1271128	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1271663	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1272773	0.85[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1677154	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1677173	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1677189	0.87[YRI][hapmap]
rs1716216	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2061761	0.84[CEU][hapmap]
rs2568884	0.91[ASN][1000 genomes]
rs2568885	0.92[AFR][1000 genomes]
rs2568887	0.84[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs2568888	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2617178	0.81[EUR][1000 genomes]
rs2617190	0.91[ASN][1000 genomes]
rs2617200	0.90[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682671	0.90[AFR][1000 genomes]
rs2682677	0.87[AFR][1000 genomes]
rs2682679	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2682695	0.84[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs2682697	0.87[ASN][1000 genomes]
rs708212	0.85[CEU][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs708215	0.83[AFR][1000 genomes]
rs708217	0.84[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs71440988	0.81[ASN][1000 genomes]
rs792875	0.83[AFR][1000 genomes]
rs793146	0.87[ASN][1000 genomes]
rs793148	0.84[CEU][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs793149	0.90[AFR][1000 genomes]
rs793150	0.85[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes]
rs793158	0.90[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs793161	0.85[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs793171	0.90[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793173	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs793174	0.84[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793175	0.86[AFR][1000 genomes]
rs793176	0.85[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793177	0.83[CEU][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs793180	0.87[ASN][1000 genomes]
rs793184	0.91[ASN][1000 genomes]
rs793186	0.84[CEU][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes]
rs976874	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][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	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31660000-31674600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:31667800-31675400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:31667800-31687600	Weak transcription	Pancreas	Pancrea
4	chr12:31669800-31677800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr12:31670000-31674800	Enhancers	HUVEC	blood vessel
6	chr12:31670000-31675400	Enhancers	Fetal Kidney	kidney
7	chr12:31670000-31675400	Enhancers	Fetal Lung	lung
8	chr12:31670000-31676400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:31670200-31676800	Enhancers	Fetal Heart	heart
10	chr12:31671000-31680200	Weak transcription	Right Atrium	heart
11	chr12:31671200-31675400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:31671400-31675200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:31671400-31677600	Enhancers	GM12878-XiMat	blood
14	chr12:31671600-31675200	Enhancers	NHEK	skin
15	chr12:31671800-31677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr12:31672000-31674600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:31672000-31678600	Weak transcription	Left Ventricle	heart
18	chr12:31672200-31674600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:31672200-31675000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:31672200-31678400	Weak transcription	Adipose Nuclei	Adipose
21	chr12:31672200-31678600	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:31672200-31680000	Weak transcription	Right Ventricle	heart
23	chr12:31672400-31676000	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr12:31672400-31676600	Enhancers	Hela-S3	cervix
25	chr12:31672400-31677200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:31672600-31674800	Weak transcription	HepG2	liver
27	chr12:31672600-31675000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr12:31672600-31675400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr12:31672600-31677600	Weak transcription	Brain Angular Gyrus	brain
30	chr12:31672600-31679000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:31672800-31674600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:31672800-31677800	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:31672800-31681000	Weak transcription	Brain Anterior Caudate	brain
34	chr12:31673000-31674200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:31673000-31674400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:31673000-31674600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:31673000-31674600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:31673000-31674600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:31673000-31674600	Weak transcription	Psoas Muscle	Psoas
40	chr12:31673000-31675000	Weak transcription	Fetal Stomach	stomach
41	chr12:31673000-31675000	Weak transcription	Ovary	ovary
42	chr12:31673000-31675400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:31673000-31677200	Weak transcription	HSMMtube	muscle
44	chr12:31673000-31678000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:31673000-31678000	Weak transcription	Fetal Brain Female	brain
46	chr12:31673000-31684600	Weak transcription	Aorta	Aorta
47	chr12:31673000-31685200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr12:31673200-31674600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:31673200-31674600	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:31673200-31674600	Weak transcription	Fetal Intestine Large	intestine

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