Variant report

Variant	rs12162238
Chromosome Location	chr19:38082385-38082386
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38081627..38083725-chr19:38083732..38085757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171817	Chromatin interaction
ENSG00000180479	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11083427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11083430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1128327	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11665759	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11666662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11666738	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs11672440	0.87[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs12151280	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes]
rs12459013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460230	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12462271	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12462505	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1478462	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17303301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17305326	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2045911	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126976	0.92[ASN][1000 genomes]
rs2279150	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2290999	1.00[CEU][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes]
rs241952	0.82[CEU][hapmap]
rs241955	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs35205379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59426132	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73031309	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73031321	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73031322	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73031326	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033117	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033129	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033139	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73033145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73035158	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035164	0.96[EUR][1000 genomes]
rs73037036	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73039018	0.82[AMR][1000 genomes];0.85[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	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38069800-38084600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:38072400-38084600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:38075200-38084600	Weak transcription	Fetal Heart	heart
4	chr19:38077200-38084600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:38078200-38084400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:38078200-38084600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:38078200-38084600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:38078600-38084600	Weak transcription	Thymus	Thymus
9	chr19:38078800-38084600	Weak transcription	Colonic Mucosa	Colon
10	chr19:38079600-38083200	Weak transcription	Psoas Muscle	Psoas
11	chr19:38079600-38083600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:38079600-38084600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:38079600-38084600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:38080000-38084400	Weak transcription	Left Ventricle	heart
15	chr19:38080200-38084600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:38080400-38084600	Weak transcription	Small Intestine	intestine
17	chr19:38080600-38083000	Weak transcription	Fetal Kidney	kidney
18	chr19:38080600-38084400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:38080800-38082800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:38081600-38084400	Weak transcription	Placenta	Placenta
21	chr19:38082000-38082400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:38082000-38082400	ZNF genes & repeats	Brain Hippocampus Middle	brain
23	chr19:38082000-38082400	ZNF genes & repeats	Fetal Lung	lung
24	chr19:38082000-38082400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
25	chr19:38082000-38083200	ZNF genes & repeats	Primary T cells from cord blood	blood
26	chr19:38082000-38083800	ZNF genes & repeats	Liver	Liver
27	chr19:38082000-38084000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:38082000-38084000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
29	chr19:38082200-38083400	Weak transcription	Brain Substantia Nigra	brain

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