Variant report

Variant	rs12257419
Chromosome Location	chr10:52193650-52193651
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52184358..52187257-chr10:52191960..52194304,3	K562	blood:
2	chr10:52189329..52191710-chr10:52192789..52194916,2	K562	blood:
3	chr10:52193457..52195166-chr10:52196882..52200363,3	K562	blood:
4	chr10:52191418..52195182-chr10:52381701..52384353,3	MCF-7	breast:
5	chr10:52187426..52191274-chr10:52192997..52195335,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10490963	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10490964	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11005626	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11005832	0.85[YRI][hapmap]
rs11005959	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203375	0.83[YRI][hapmap]
rs1203410	0.83[YRI][hapmap]
rs1203421	0.80[YRI][hapmap]
rs12246361	0.85[YRI][hapmap]
rs12262259	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12264817	0.85[YRI][hapmap]
rs1369860	0.83[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17438825	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17440448	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17518471	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17519121	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17519380	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17721658	0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17721694	0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17721713	0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17778152	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1916568	0.82[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1916569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1916571	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060560	0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2064759	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2117961	0.84[ASN][1000 genomes]
rs2117962	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255387	0.81[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2255720	0.92[ASN][1000 genomes]
rs2255849	0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2255853	0.83[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2255859	0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2574955	0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2574956	0.83[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2574975	0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2574981	0.92[ASN][1000 genomes]
rs2688875	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs2688877	0.86[ASN][1000 genomes]
rs2688879	0.83[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2842102	0.92[ASN][1000 genomes]
rs2842105	0.92[ASN][1000 genomes]
rs2842106	0.92[ASN][1000 genomes]
rs2842107	0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2842109	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34672995	1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34928652	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3802537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4935152	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935673	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4935703	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4935713	0.92[ASN][1000 genomes]
rs4935729	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4935731	0.81[AMR][1000 genomes]
rs4935732	0.81[AMR][1000 genomes]
rs55773344	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55861418	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56078228	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56080689	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56133398	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56225400	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56268559	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56277433	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56403030	0.81[AMR][1000 genomes]
rs61559519	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61741330	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61856761	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61856763	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61856778	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61856782	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61856787	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61856788	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61856793	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61856794	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61856795	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61856828	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61856832	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61858062	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858064	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61858065	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61858068	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61858069	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61858206	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61858207	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7067626	1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7068430	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7069115	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7082805	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7092753	0.96[ASN][1000 genomes]
rs7099450	0.85[EUR][1000 genomes]
rs72801752	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72801754	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72801768	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72801775	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72801776	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72801781	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7392702	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7475420	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7893281	0.83[EUR][1000 genomes]
rs7921632	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs884880	1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs920136	0.83[YRI][hapmap]
rs9988708	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
4	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
5	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
11	chr10:52180600-52194000	Weak transcription	Fetal Intestine Large	intestine
12	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
13	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
15	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
16	chr10:52189800-52194400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr10:52191000-52193800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr10:52191200-52196400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr10:52191400-52200400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr10:52191800-52197000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr10:52191800-52205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
25	chr10:52192000-52196200	Weak transcription	Brain Substantia Nigra	brain
26	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
27	chr10:52192200-52193800	Strong transcription	K562	blood
28	chr10:52192200-52196200	Weak transcription	Primary T cells from cord blood	blood
29	chr10:52192200-52197000	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr10:52192400-52194800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr10:52192400-52196200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr10:52192400-52196400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:52192400-52196800	Weak transcription	Brain Anterior Caudate	brain
34	chr10:52192400-52196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:52192400-52197000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr10:52192400-52198200	Weak transcription	Right Atrium	heart
37	chr10:52192400-52199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr10:52192400-52199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:52192400-52200800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr10:52192400-52202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr10:52192400-52219400	Weak transcription	Liver	Liver
43	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
47	chr10:52192400-52230400	Weak transcription	HSMM	muscle
48	chr10:52193000-52194000	Enhancers	GM12878-XiMat	blood
49	chr10:52193000-52197400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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