Variant report

Variant	rs10842420
Chromosome Location	chr12:25015770-25015771
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10160847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10466757	0.84[ASN][1000 genomes]
rs10466800	0.83[ASN][1000 genomes]
rs1054277	0.89[JPT][hapmap]
rs1054279	0.89[JPT][hapmap]
rs1075063	0.91[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap]
rs10771127	0.89[JPT][hapmap]
rs10771134	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771138	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10842417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11047677	0.83[AFR][1000 genomes]
rs11047684	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11047686	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11047689	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs11609552	0.86[JPT][hapmap]
rs11613673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11613710	0.99[ASN][1000 genomes]
rs11615863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12227952	0.83[ASN][1000 genomes]
rs12228257	0.84[ASN][1000 genomes]
rs12229422	0.84[ASN][1000 genomes]
rs12296255	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12301149	0.99[ASN][1000 genomes]
rs12302883	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12319639	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12424348	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12425320	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1392195	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1392196	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1471844	0.89[JPT][hapmap]
rs16928089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17372766	0.84[ASN][1000 genomes]
rs1872644	0.89[JPT][hapmap]
rs1872645	0.89[JPT][hapmap]
rs2046524	0.89[JPT][hapmap]
rs2062497	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2133582	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2133583	0.99[ASN][1000 genomes]
rs2133584	0.91[ASN][1000 genomes]
rs2200509	0.89[JPT][hapmap]
rs2220269	0.89[JPT][hapmap]
rs2220271	0.92[ASN][1000 genomes]
rs2353478	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2353483	0.89[JPT][hapmap]
rs3198082	0.89[JPT][hapmap]
rs3736211	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4522264	0.84[CHB][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs4963805	0.82[ASN][1000 genomes]
rs4963806	0.82[ASN][1000 genomes]
rs4963808	0.81[ASN][1000 genomes]
rs4963814	0.95[ASN][1000 genomes]
rs60104197	0.84[ASN][1000 genomes]
rs61914865	0.80[ASN][1000 genomes]
rs6487419	0.89[JPT][hapmap]
rs6487420	1.00[JPT][hapmap]
rs6487434	0.96[CEU][hapmap];0.92[CHB][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6487437	1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7138685	0.84[ASN][1000 genomes]
rs718567	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs7296211	0.89[JPT][hapmap]
rs7305794	0.89[JPT][hapmap]
rs73061805	0.95[ASN][1000 genomes]
rs73061812	0.93[ASN][1000 genomes]
rs73061817	0.88[ASN][1000 genomes]
rs73079552	0.91[ASN][1000 genomes]
rs73079568	0.97[ASN][1000 genomes]
rs73079570	0.99[ASN][1000 genomes]
rs7308285	0.86[ASN][1000 genomes]
rs7310300	0.89[JPT][hapmap]
rs7961152	0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.82[ASN][1000 genomes]
rs7961688	0.93[ASN][1000 genomes]
rs7962203	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7973974	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs7976928	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.84[ASN][1000 genomes]
rs937503	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs954199	0.84[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs954201	0.83[CHB][hapmap];0.81[JPT][hapmap];0.80[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv898920	chr12:24648863-25147192	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv1053309	chr12:24770995-25078227	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	22 gene(s)	inside rSNPs	diseases
8	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv1045302	chr12:24921100-25078227	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
17	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
18	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
19	nsv1054863	chr12:24941350-25078227	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
20	nsv541426	chr12:24941350-25078227	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
21	nsv1051968	chr12:24941350-25138118	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	nsv541427	chr12:24941350-25138118	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
23	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
24	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
25	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
26	esv2190797	chr12:25015769-25015770	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:24968000-25017600	Weak transcription	Fetal Thymus	thymus
2	chr12:24971000-25054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:24992000-25053000	Weak transcription	Fetal Stomach	stomach
4	chr12:24992400-25033200	Weak transcription	Fetal Brain Male	brain
5	chr12:24992600-25053400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:25002600-25022200	Weak transcription	Lung	lung
7	chr12:25002800-25019200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:25005000-25019000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:25008200-25017200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:25008200-25030200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:25008800-25016200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:25008800-25016600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:25009000-25016400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:25009000-25017000	Weak transcription	HMEC	breast
15	chr12:25009000-25017200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:25009200-25016400	Weak transcription	NH-A	brain
17	chr12:25009200-25017000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:25009200-25017200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:25009400-25017000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr12:25009400-25017000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:25010400-25016000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
22	chr12:25011200-25026600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:25011600-25017200	Weak transcription	Pancreas	Pancrea
24	chr12:25012400-25017400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:25012600-25016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:25013000-25015800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:25013000-25018400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:25013800-25016400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:25014000-25016800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr12:25014000-25019000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr12:25014000-25028000	Weak transcription	Brain Germinal Matrix	brain
32	chr12:25014200-25016600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr12:25014400-25015800	Genic enhancers	HUVEC	blood vessel
34	chr12:25014400-25016400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:25014400-25042800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:25014600-25015800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr12:25014600-25015800	Enhancers	HSMMtube	muscle
38	chr12:25014600-25016400	Enhancers	GM12878-XiMat	blood
39	chr12:25014600-25017200	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:25014800-25017400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr12:25014800-25017400	Strong transcription	Dnd41	blood
42	chr12:25015200-25015800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:25015200-25016000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr12:25015200-25016800	Strong transcription	Fetal Muscle Leg	muscle
45	chr12:25015400-25015800	Strong transcription	Primary hematopoietic stem cells	blood
46	chr12:25015400-25016000	Strong transcription	HSMM	muscle
47	chr12:25015400-25016600	Weak transcription	Placenta	Placenta
48	chr12:25015400-25017200	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:25015400-25017400	ZNF genes & repeats	K562	blood
50	chr12:25015600-25016600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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