Variant report

Variant	rs11238553
Chromosome Location	chr10:43971441-43971442
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:43970982..43973705-chr10:43978216..43981135,2	K562	blood:
2	chr10:43971059..43972793-chr10:43982903..43984955,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

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];0.80[ASN][1000 genomes]
rs10899794	0.89[JPT][hapmap]
rs10899796	0.87[EUR][1000 genomes]
rs10899797	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs10899800	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10899801	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899802	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899803	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]
rs10899806	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899808	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11238530	0.92[AMR][1000 genomes]
rs11238532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[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];0.80[ASN][1000 genomes]
rs11238558	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11238566	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238572	0.88[ASN][1000 genomes]
rs11525297	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11814409	0.85[CHB][hapmap];0.84[YRI][hapmap]
rs11815101	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[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];0.80[ASN][1000 genomes]
rs12220528	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12245541	0.88[EUR][1000 genomes];0.90[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];0.80[ASN][1000 genomes]
rs12254798	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12261855	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12262836	0.85[ASN][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];0.80[ASN][1000 genomes]
rs13376924	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4948726	0.90[JPT][hapmap]
rs57059251	0.82[ASN][1000 genomes]
rs6593513	0.80[JPT][hapmap]
rs7099802	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7905676	0.90[JPT][hapmap]
rs7907179	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1046236	chr10:43968075-44012933	ZNF genes & repeats Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43952000-43972600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:43952000-43973200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:43952000-43977200	Weak transcription	HSMMtube	muscle
4	chr10:43952200-43975200	Weak transcription	Fetal Stomach	stomach
5	chr10:43952400-43976200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr10:43957800-43971800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr10:43957800-43976600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr10:43957800-43977200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr10:43962800-43976400	Weak transcription	Primary T cells from cord blood	blood
10	chr10:43966600-43976400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr10:43967000-43976400	Weak transcription	Aorta	Aorta
12	chr10:43967200-43972000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:43967400-43978600	Weak transcription	Pancreas	Pancrea
14	chr10:43968000-43976400	Weak transcription	Ovary	ovary
15	chr10:43968200-43974800	Weak transcription	Fetal Intestine Small	intestine
16	chr10:43968800-43977200	Weak transcription	Brain Hippocampus Middle	brain
17	chr10:43969000-43977000	Weak transcription	Brain Anterior Caudate	brain
18	chr10:43969400-43977200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr10:43969600-43977200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:43969800-43978200	Weak transcription	Fetal Kidney	kidney
21	chr10:43970600-43973400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr10:43971000-43972400	Strong transcription	Liver	Liver
23	chr10:43971200-43971600	Strong transcription	Lung	lung
24	chr10:43971200-43971600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr10:43971200-43972000	Strong transcription	Primary B cells from cord blood	blood
26	chr10:43971200-43976400	Weak transcription	Colon Smooth Muscle	Colon
27	chr10:43971400-43972200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr10:43971400-43972200	Strong transcription	Adipose Nuclei	Adipose
29	chr10:43971400-43972200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr10:43971400-43974800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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