Variant report

Variant	rs10408356
Chromosome Location	chr19:40804559-40804560
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	chr19:40790403..40792458-chr19:40802538..40805158,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKT2-2	chr19:40804388-40805930	NONHSAT066369

Variant related genes	Relation type
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10415181	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10416620	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10418932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10419465	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10420842	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10422343	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10423896	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12151243	0.85[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16974157	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2163840	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2304188	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28362958	0.91[ASN][1000 genomes]
rs28667591	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34716810	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55862427	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57885763	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58336440	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58613082	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59010363	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59343080	0.82[ASN][1000 genomes]
rs60869669	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61685259	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107590	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62107593	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62107594	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62107630	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62107631	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7247916	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7248861	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7254617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73044533	0.86[ASN][1000 genomes]
rs8100207	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8111619	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112998	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs892118	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs892119	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs892120	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9304588	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304589	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs934426	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv3386713	chr19:40794161-40828617	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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 miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40792000-40807600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:40792000-40811400	Weak transcription	Brain Anterior Caudate	brain
3	chr19:40792000-40826200	Weak transcription	Hela-S3	cervix
4	chr19:40792200-40807600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:40792200-40810200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr19:40792200-40821400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:40792200-40821400	Weak transcription	Fetal Intestine Small	intestine
8	chr19:40793000-40805400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:40793000-40810200	Weak transcription	Adipose Nuclei	Adipose
10	chr19:40793000-40821400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:40793000-40822000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr19:40793200-40820600	Weak transcription	HSMM	muscle
13	chr19:40793200-40820800	Weak transcription	Dnd41	blood
14	chr19:40793200-40822000	Weak transcription	Fetal Stomach	stomach
15	chr19:40793800-40821800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr19:40800400-40826400	Weak transcription	Brain Angular Gyrus	brain
17	chr19:40800800-40822000	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:40802800-40828000	Weak transcription	NH-A	brain
19	chr19:40803000-40822000	Weak transcription	Lung	lung
20	chr19:40803200-40805000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr19:40803800-40822000	Weak transcription	Primary T cells from cord blood	blood

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