Variant report

Variant	rs1203421
Chromosome Location	chr10:52183772-52183773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52182601..52184931-chr10:52195030..52197697,2	K562	blood:
2	chr10:52182056..52184525-chr10:52364290..52366109,2	MCF-7	breast:
3	chr10:52176794..52179947-chr10:52182288..52185320,3	K562	blood:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction
ENSG00000230036	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10825780	0.81[JPT][hapmap]
rs11005626	0.85[YRI][hapmap]
rs11005832	0.95[YRI][hapmap]
rs11006194	0.84[CHB][hapmap]
rs1203375	0.82[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1203377	0.96[EUR][1000 genomes]
rs1203382	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[ASN][1000 genomes]
rs1203386	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203390	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1203393	0.93[ASN][1000 genomes]
rs1203394	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203395	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203401	0.93[ASN][1000 genomes]
rs1203403	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203405	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203407	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203409	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203410	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203411	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203413	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1203415	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs1203418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12246361	0.95[YRI][hapmap]
rs12257419	0.80[YRI][hapmap]
rs12260887	0.85[YRI][hapmap]
rs12264511	0.86[YRI][hapmap]
rs12264817	0.95[YRI][hapmap]
rs12267134	0.86[YRI][hapmap]
rs1740761	0.86[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs1810576	0.90[ASN][1000 genomes]
rs1916566	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs1916567	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2099527	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2117958	0.93[EUR][1000 genomes]
rs2221	0.80[CEU][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs2339402	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2574985	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2688878	0.88[EUR][1000 genomes]
rs2842103	0.91[CEU][hapmap];0.92[EUR][1000 genomes]
rs2842108	0.83[EUR][1000 genomes]
rs2842111	0.92[EUR][1000 genomes]
rs2983347	0.90[ASN][1000 genomes]
rs2983350	0.92[JPT][hapmap]
rs2983354	0.82[CEU][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs2983357	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs2983359	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2983361	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2983368	0.82[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2983369	0.91[ASN][1000 genomes]
rs2983370	0.81[ASN][1000 genomes]
rs2983371	0.91[ASN][1000 genomes]
rs3011771	0.91[ASN][1000 genomes]
rs3011773	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3011779	0.85[ASN][1000 genomes]
rs3011780	0.85[ASN][1000 genomes]
rs3011782	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs3011783	0.83[ASN][1000 genomes]
rs3011787	0.81[CEU][hapmap];0.91[ASN][1000 genomes]
rs3011788	0.82[CEU][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011789	0.80[ASN][1000 genomes]
rs3011790	0.84[JPT][hapmap]
rs3011791	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011792	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011793	0.80[ASN][1000 genomes]
rs3011794	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3011797	0.85[JPT][hapmap]
rs3011801	0.85[JPT][hapmap]
rs4312019	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs4536155	0.96[EUR][1000 genomes]
rs7068377	0.91[YRI][hapmap]
rs7092014	0.93[EUR][1000 genomes]
rs715675	0.96[EUR][1000 genomes]
rs7912351	0.84[ASN][1000 genomes]
rs920136	0.86[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9988708	0.90[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:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52188800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
5	chr10:52178800-52183800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr10:52178800-52187400	Weak transcription	Primary T cells from cord blood	blood
7	chr10:52178800-52191200	Weak transcription	HSMMtube	muscle
8	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
9	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:52179000-52191000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:52179000-52191200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:52179000-52191400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr10:52179000-52191600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:52180000-52185000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr10:52180000-52189800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr10:52180000-52190800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
22	chr10:52180600-52194000	Weak transcription	Fetal Intestine Large	intestine
23	chr10:52181400-52184000	Enhancers	Liver	Liver
24	chr10:52181400-52191000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr10:52181600-52184000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr10:52181600-52184800	Weak transcription	Primary B cells from cord blood	blood
27	chr10:52181600-52187200	Weak transcription	K562	blood
28	chr10:52181600-52187800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr10:52181600-52189800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr10:52181600-52190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
32	chr10:52181800-52183800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:52182000-52191200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr10:52182200-52184000	Enhancers	Brain Anterior Caudate	brain
36	chr10:52182200-52186200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr10:52182200-52191000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr10:52182200-52191400	Weak transcription	Psoas Muscle	Psoas
39	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
40	chr10:52182400-52189800	Weak transcription	Adipose Nuclei	Adipose
41	chr10:52182600-52191000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr10:52182600-52191000	Weak transcription	Fetal Lung	lung
43	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
44	chr10:52183000-52191200	Weak transcription	Brain Angular Gyrus	brain
45	chr10:52183200-52186200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr10:52183200-52189600	Weak transcription	Brain Substantia Nigra	brain
47	chr10:52183400-52190000	Weak transcription	Brain Hippocampus Middle	brain
48	chr10:52183400-52190600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr10:52183400-52191400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr10:52183600-52184200	Enhancers	Pancreatic Islets	Pancreatic Islet

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