Variant report

Variant	rs1253401
Chromosome Location	chr10:99050270-99050271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99050239..99051953-chr10:99089208..99091250,2	K562	blood:
2	chr10:99049975..99053832-chr10:99093402..99096465,5	K562	blood:
3	chr10:99048545..99053546-chr10:99092341..99096465,6	K562	blood:
4	chr10:99044514..99046643-chr10:99048334..99050746,3	K562	blood:

Variant related genes	Relation type
ENSG00000181274	Chromatin interaction
ENSG00000225850	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1088187	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11189121	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs12240590	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs1253386	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1253387	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1253396	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253397	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1253400	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12769073	0.85[EUR][1000 genomes]
rs12782676	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13439	0.84[CEU][hapmap]
rs2484880	0.84[CEU][hapmap]
rs2861877	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2992773	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34115590	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34288920	0.87[EUR][1000 genomes]
rs34624597	0.87[EUR][1000 genomes]
rs36098270	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4917765	0.86[EUR][1000 genomes]
rs61569149	0.81[EUR][1000 genomes]
rs61861842	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61861843	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61861844	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61861849	0.85[EUR][1000 genomes]
rs61861850	0.88[EUR][1000 genomes]
rs701821	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7074896	0.85[EUR][1000 genomes]
rs7091162	0.85[EUR][1000 genomes]
rs7101333	0.86[EUR][1000 genomes]
rs7915926	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793515	0.89[CEU][hapmap]
rs793519	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs793520	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs793522	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793524	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs793531	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs796980	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs946981	0.84[CEU][hapmap]

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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1041614	chr10:98928281-99083056	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1045553	chr10:98944397-99122203	Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv540750	chr10:98944397-99122203	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv831952	chr10:98998344-99145924	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv895914	chr10:99006083-99131676	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv7507	chr10:99031233-99070690	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv975787	chr10:99048466-99061224	Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98978600-99051800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:98987200-99051200	Weak transcription	Pancreas	Pancrea
3	chr10:99019400-99051600	Weak transcription	Ovary	ovary
4	chr10:99021400-99051000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr10:99023600-99051200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr10:99024000-99050800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:99024800-99051200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:99025800-99050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr10:99026000-99051200	Weak transcription	Primary T cells from cord blood	blood
10	chr10:99028600-99051200	Weak transcription	Small Intestine	intestine
11	chr10:99031400-99050400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:99038000-99050400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr10:99038800-99051200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr10:99038800-99051200	Weak transcription	Brain Germinal Matrix	brain
15	chr10:99038800-99051200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:99038800-99051200	Weak transcription	NH-A	brain
17	chr10:99038800-99051400	Weak transcription	Brain Angular Gyrus	brain
18	chr10:99039000-99050600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr10:99039000-99050800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr10:99039000-99051200	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:99039000-99051200	Weak transcription	HUVEC	blood vessel
22	chr10:99039000-99051400	Weak transcription	Brain Anterior Caudate	brain
23	chr10:99039400-99051200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr10:99039400-99051200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:99039400-99051200	Weak transcription	NHEK	skin
26	chr10:99039400-99051400	Weak transcription	Adipose Nuclei	Adipose
27	chr10:99039600-99050800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr10:99039600-99051000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:99039600-99051000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr10:99039600-99051200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:99039800-99050800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr10:99039800-99051200	Weak transcription	NHDF-Ad	bronchial
33	chr10:99040400-99050400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:99041200-99051600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr10:99042000-99051000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr10:99042400-99050800	Weak transcription	GM12878-XiMat	blood
37	chr10:99042600-99051400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr10:99043600-99051200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr10:99044400-99051600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:99045000-99051200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr10:99045800-99051200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr10:99045800-99051600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr10:99046400-99051400	Weak transcription	Right Ventricle	heart
44	chr10:99047200-99051200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr10:99047400-99050800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr10:99047400-99050800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr10:99047400-99050800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr10:99047400-99050800	Weak transcription	Fetal Intestine Large	intestine
49	chr10:99047400-99051000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr10:99047400-99051200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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