Variant report

Variant	rs10899803
Chromosome Location	chr10:43940898-43940899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43939246..43942675-chr10:43946277..43949309,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243660	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899791	0.84[ASN][1000 genomes]
rs10899793	0.84[ASN][1000 genomes]
rs10899794	0.89[JPT][hapmap]
rs10899796	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10899797	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10899800	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899801	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899802	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10899808	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238525	0.82[ASN][1000 genomes]
rs11238530	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11238532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238553	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238558	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238566	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11238572	0.92[AMR][1000 genomes]
rs11525297	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11814409	0.85[CHB][hapmap];0.84[YRI][hapmap]
rs11815101	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12217904	0.82[YRI][hapmap]
rs12220230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12220528	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12245541	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12250140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12254798	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12261855	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12262836	0.92[AMR][1000 genomes]
rs13376803	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13376924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17153534	0.84[ASN][1000 genomes]
rs17153701	0.86[ASW][hapmap]
rs2247979	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2247981	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2250444	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs2252783	0.80[JPT][hapmap]
rs2261636	0.90[JPT][hapmap]
rs28865415	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4648316	0.84[ASN][1000 genomes]
rs4948726	0.90[JPT][hapmap]
rs59383062	0.84[ASN][1000 genomes]
rs59806733	0.85[ASN][1000 genomes]
rs6593513	0.80[JPT][hapmap]
rs7099802	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7905676	0.90[JPT][hapmap]
rs7907179	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7921001	0.82[ASN][1000 genomes]

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	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv895087	chr10:43783339-43982390	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv831842	chr10:43846541-43987501	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv895088	chr10:43871999-44003101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv825354	chr10:43883418-43949936	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv825356	chr10:43893080-43946515	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases
7	esv3448813	chr10:43919995-43950867	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv1043746	chr10:43940898-43977155	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43933000-43947200	Weak transcription	Spleen	Spleen
2	chr10:43933000-43949600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr10:43933000-43950200	Weak transcription	Lung	lung
4	chr10:43933200-43947600	Weak transcription	Brain Anterior Caudate	brain
5	chr10:43933200-43948000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:43933200-43950000	Weak transcription	Brain Substantia Nigra	brain
7	chr10:43933200-43950200	Weak transcription	Brain Angular Gyrus	brain
8	chr10:43933200-43950200	Weak transcription	Brain Hippocampus Middle	brain
9	chr10:43933200-43950200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr10:43933200-43950200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr10:43933400-43948000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:43933600-43947200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:43933600-43947400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:43933600-43948200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr10:43933600-43948200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:43933600-43949800	Weak transcription	Adipose Nuclei	Adipose
17	chr10:43933800-43946600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr10:43934200-43942200	Weak transcription	Fetal Lung	lung
19	chr10:43934200-43949200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr10:43936400-43943800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr10:43936400-43950000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:43936600-43946000	Weak transcription	Primary B cells from cord blood	blood
23	chr10:43936800-43941800	Weak transcription	Fetal Stomach	stomach
24	chr10:43936800-43944200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr10:43938600-43948000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:43939600-43941200	Enhancers	NHEK	skin
27	chr10:43940000-43941000	Enhancers	HepG2	liver
28	chr10:43940000-43941200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr10:43940000-43943800	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr10:43940000-43946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr10:43940200-43941000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr10:43940200-43941000	Enhancers	Stomach Mucosa	stomach
33	chr10:43940200-43950200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr10:43940400-43941000	Enhancers	A549	lung
35	chr10:43940400-43943800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr10:43940400-43950200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:43940400-43950200	Weak transcription	Colonic Mucosa	Colon
38	chr10:43940800-43944800	Weak transcription	Primary T cells from cord blood	blood
39	chr10:43940800-43947200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr10:43940800-43949600	Weak transcription	Hela-S3	cervix
41	chr10:43940800-43950600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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