Variant report

Variant	rs826853
Chromosome Location	chr12:39114259-39114260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10160990	1.00[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs10732735	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs1095573	1.00[CEU][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs1095576	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1095578	0.85[CEU][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs11168929	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169037	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169056	0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169105	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169324	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169604	0.85[AFR][1000 genomes]
rs11169615	0.82[EUR][1000 genomes]
rs11169618	0.82[EUR][1000 genomes]
rs11537523	0.82[EUR][1000 genomes]
rs11559976	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12231800	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1356267	0.85[CEU][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs1486342	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1486343	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1486355	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1523119	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1523120	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1533918	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs1607040	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1615648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1621487	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1684397	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1684405	0.82[AMR][1000 genomes]
rs1684426	0.84[AFR][1000 genomes]
rs1719833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1719847	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1914052	0.85[CEU][hapmap];0.89[JPT][hapmap]
rs1996879	0.82[EUR][1000 genomes]
rs2069210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2134398	0.81[AMR][1000 genomes]
rs2455609	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2455610	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2630776	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630778	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630780	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2630782	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2653722	0.82[EUR][1000 genomes]
rs2653738	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2653752	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2653754	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2653760	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2653761	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2653769	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2653775	0.81[AMR][1000 genomes]
rs2730897	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2730901	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2730908	0.80[AMR][1000 genomes]
rs2730910	0.82[CEU][hapmap];0.94[JPT][hapmap]
rs2730944	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2730946	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2730948	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2730949	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2730954	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2730955	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2730957	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2730964	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4002228	0.81[EUR][1000 genomes]
rs4494337	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4768394	0.90[JPT][hapmap];0.83[TSI][hapmap]
rs60368384	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68075931	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7298168	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs73269131	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7978838	0.90[JPT][hapmap]
rs8181763	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8181765	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826839	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826840	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826841	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826845	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826846	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs826847	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs826854	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826860	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs826861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826863	0.82[AMR][1000 genomes]
rs826865	0.92[ASN][1000 genomes]
rs826866	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826867	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826868	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs826871	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs826878	0.84[YRI][hapmap]
rs826880	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826882	0.85[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes]
rs826884	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs826885	0.84[EUR][1000 genomes]
rs826887	0.93[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs826890	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs826894	0.82[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs826895	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs826896	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs851933	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs862331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs862332	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs866120	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv469356	chr12:38242029-39187408	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv558574	chr12:38242029-39187408	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv1039538	chr12:38640895-39180750	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1039821	chr12:38959645-39121578	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1053316	chr12:38959645-39122853	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1043831	chr12:38979065-39117868	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv541479	chr12:38979065-39117868	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
3	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
4	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr12:39079200-39114400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:39080600-39115600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:39086000-39114400	Weak transcription	Aorta	Aorta
8	chr12:39092600-39153600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:39094600-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:39095800-39114600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:39095800-39117800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:39109800-39116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:39110400-39114600	Weak transcription	Adipose Nuclei	Adipose
14	chr12:39110800-39119800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:39111000-39115600	Weak transcription	GM12878-XiMat	blood
16	chr12:39111400-39114600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:39111400-39115200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:39111800-39114600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr12:39111800-39119400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:39112000-39114400	Weak transcription	Lung	lung
21	chr12:39112400-39115200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:39112400-39118400	Weak transcription	Fetal Intestine Small	intestine
23	chr12:39112800-39114400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:39113000-39114600	Weak transcription	Esophagus	oesophagus
25	chr12:39113000-39114600	Weak transcription	Spleen	Spleen
26	chr12:39113000-39114800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:39113000-39117200	Weak transcription	Colonic Mucosa	Colon
28	chr12:39113200-39114800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr12:39113200-39116000	Strong transcription	Left Ventricle	heart
30	chr12:39113400-39115400	Weak transcription	Ovary	ovary
31	chr12:39113800-39115400	Weak transcription	Fetal Intestine Large	intestine
32	chr12:39113800-39117000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:39113800-39117600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:39113800-39118400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:39113800-39123800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:39114000-39115600	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:39114000-39115800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:39114000-39115800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:39114000-39117200	Weak transcription	Fetal Stomach	stomach
40	chr12:39114000-39118400	Strong transcription	Liver	Liver
41	chr12:39114200-39115800	Strong transcription	Right Ventricle	heart
42	chr12:39114200-39133600	Weak transcription	A549	lung

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