Variant report

Variant	rs10414396
Chromosome Location	chr19:42970165-42970166
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	chr19:42968131..42971103-chr19:42973928..42976779,2	MCF-7	breast:

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10401178	1.00[CEU][hapmap];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	1.00[CEU][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10405037	0.90[AMR][1000 genomes]
rs10405152	1.00[CEU][hapmap];0.90[YRI][hapmap];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]
rs10405410	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs10406227	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]
rs10415284	0.90[AMR][1000 genomes]
rs10416108	1.00[CEU][hapmap];0.81[YRI][hapmap]
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]
rs10424206	1.00[CEU][hapmap];0.90[YRI][hapmap]
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]
rs11878959	1.00[CEU][hapmap]
rs11878991	1.00[CEU][hapmap]
rs11880554	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11880876	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs11881583	1.00[CEU][hapmap];0.90[YRI][hapmap];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]
rs11883406	1.00[CEU][hapmap]
rs11883425	1.00[CEU][hapmap]
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	1.00[CEU][hapmap];0.89[YRI][hapmap];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	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6509019	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs7246161	1.00[CEU][hapmap]
rs7246591	1.00[CEU][hapmap]
rs7247278	1.00[CEU][hapmap];1.00[YRI][hapmap];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]
rs7258854	1.00[CEU][hapmap]
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	1.00[CEU][hapmap];1.00[YRI][hapmap];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	1.00[YRI][hapmap];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:49 , 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	chr19:42960200-42975600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:42960400-42971000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr19:42960400-42974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr19:42961000-42970200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:42961800-42970200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:42961800-42970200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:42961800-42970200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr19:42965200-42970200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr19:42965800-42972400	Enhancers	Primary B cells from peripheral blood	blood
12	chr19:42966600-42970400	Weak transcription	Stomach Mucosa	stomach
13	chr19:42966800-42970200	Weak transcription	Right Atrium	heart
14	chr19:42967000-42970200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:42967200-42970200	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr19:42967200-42970400	Weak transcription	Fetal Intestine Large	intestine
17	chr19:42967200-42970800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr19:42967200-42972400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:42967200-42972400	Weak transcription	Esophagus	oesophagus
20	chr19:42967400-42970200	Weak transcription	Brain Anterior Caudate	brain
21	chr19:42967400-42970800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:42967400-42972400	Weak transcription	Fetal Intestine Small	intestine
23	chr19:42967600-42970200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:42967600-42970200	Weak transcription	Brain Angular Gyrus	brain
25	chr19:42967600-42970200	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:42968200-42970200	Weak transcription	Brain Substantia Nigra	brain
27	chr19:42968200-42970200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr19:42969000-42972200	Enhancers	Primary B cells from cord blood	blood
29	chr19:42969200-42971000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:42969400-42971400	Flanking Active TSS	GM12878-XiMat	blood
31	chr19:42969400-42972000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr19:42969400-42973000	Enhancers	HepG2	liver
33	chr19:42969400-42975200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr19:42969800-42971400	Enhancers	Duodenum Mucosa	Duodenum
35	chr19:42969800-42971800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr19:42970000-42970200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr19:42970000-42970800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr19:42970000-42970800	Enhancers	H9 Cell Line	embryonic stem cell
39	chr19:42970000-42970800	Enhancers	Fetal Muscle Leg	muscle
40	chr19:42970000-42971000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:42970000-42971000	Enhancers	Left Ventricle	heart
42	chr19:42970000-42971600	Enhancers	Brain Cingulate Gyrus	brain
43	chr19:42970000-42971600	Enhancers	Lung	lung
44	chr19:42970000-42971600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr19:42970000-42971800	Enhancers	Adipose Nuclei	Adipose
46	chr19:42970000-42972600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:42970000-42972600	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr19:42970000-42972600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:42970000-42974600	Enhancers	Primary neutrophils fromperipheralblood	blood

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