Variant report

Variant	rs10406227
Chromosome Location	chr19:42969075-42969076
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	chr19:42957018..42958955-chr19:42966845..42969833,2	MCF-7	breast:
2	chr19:42968131..42971103-chr19:42973928..42976779,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10401178	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10402853	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404589	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405037	0.90[AMR][1000 genomes]
rs10405152	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10405179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10408822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10412074	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412173	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10412594	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414396	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10415284	0.90[AMR][1000 genomes]
rs10418090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418997	0.87[AFR][1000 genomes]
rs10419543	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10420773	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs10422191	0.87[AFR][1000 genomes]
rs10423227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423370	0.90[AMR][1000 genomes]
rs10425199	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10425666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10426304	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11880554	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11880876	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11881583	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11882291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11882701	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13343840	0.87[AFR][1000 genomes]
rs13346522	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs16975787	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975799	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16975815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975862	0.87[AFR][1000 genomes]
rs28403155	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28425201	0.86[AFR][1000 genomes]
rs28433890	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28602626	0.95[AMR][1000 genomes]
rs28625452	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28635141	0.95[AMR][1000 genomes]
rs28660279	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs41348545	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41381546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41421250	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs57018456	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58050143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58162305	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58702905	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60747186	0.85[AMR][1000 genomes]
rs61388144	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6509015	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7247278	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7248907	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7249304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7250501	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7252874	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7253634	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7256850	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs7259335	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73558492	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73558498	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73560408	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8101378	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8104731	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8105525	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8106836	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8107720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108992	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8109086	0.88[AFR][1000 genomes]
rs8110904	0.89[AMR][1000 genomes]
rs8110922	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8111171	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8111468	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8112593	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8112915	0.90[AMR][1000 genomes]
rs8113154	0.90[AMR][1000 genomes]
rs8113448	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9749434	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs9916999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9917002	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
2	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong 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	70 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42957400-42970600	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr19:42960000-42970200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:42960200-42970000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:42960400-42971000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr19:42960600-42969800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:42961000-42970200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr19:42961800-42970000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr19:42961800-42970000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:42961800-42970200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:42961800-42970200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr19:42961800-42970200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:42965200-42970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr19:42965800-42972400	Enhancers	Primary B cells from peripheral blood	blood
16	chr19:42966400-42970000	Weak transcription	Left Ventricle	heart
17	chr19:42966600-42969400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:42966600-42970000	Weak transcription	Adipose Nuclei	Adipose
19	chr19:42966600-42970000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr19:42966600-42970400	Weak transcription	Stomach Mucosa	stomach
21	chr19:42966800-42970200	Weak transcription	Right Atrium	heart
22	chr19:42967000-42969200	Weak transcription	GM12878-XiMat	blood
23	chr19:42967000-42970000	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr19:42967000-42970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:42967200-42970200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr19:42967200-42970400	Weak transcription	Fetal Intestine Large	intestine
27	chr19:42967200-42970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr19:42967200-42972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr19:42967200-42972400	Weak transcription	Esophagus	oesophagus
30	chr19:42967400-42969400	Weak transcription	HepG2	liver
31	chr19:42967400-42970200	Weak transcription	Brain Anterior Caudate	brain
32	chr19:42967400-42970800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:42967400-42972400	Weak transcription	Fetal Intestine Small	intestine
34	chr19:42967600-42970200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:42967600-42970200	Weak transcription	Brain Angular Gyrus	brain
36	chr19:42967600-42970200	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:42968200-42970200	Weak transcription	Brain Substantia Nigra	brain
38	chr19:42968200-42970200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr19:42968400-42970000	Weak transcription	Brain Cingulate Gyrus	brain
40	chr19:42969000-42972200	Enhancers	Primary B cells from cord blood	blood

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