Variant report

Variant	rs10411574
Chromosome Location	chr19:38001879-38001880
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37996541..38000346-chr19:38000524..38005136,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266916	Chromatin interaction
ENSG00000188227	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1015848	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1015849	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1035479	0.82[EUR][1000 genomes]
rs10403582	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10404945	0.91[EUR][1000 genomes]
rs10405325	0.83[EUR][1000 genomes]
rs10406177	0.85[EUR][1000 genomes]
rs10407084	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10409204	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10413602	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10420430	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10420722	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420754	0.91[EUR][1000 genomes]
rs10422074	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10422667	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10426618	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11083426	0.95[EUR][1000 genomes]
rs12972252	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12979470	0.87[EUR][1000 genomes]
rs12981532	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13343471	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13343502	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1382357	0.93[EUR][1000 genomes]
rs2045908	0.93[EUR][1000 genomes]
rs2081096	0.91[EUR][1000 genomes]
rs2112920	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2112922	0.86[EUR][1000 genomes]
rs2112923	0.89[EUR][1000 genomes]
rs2126977	0.94[EUR][1000 genomes]
rs2279148	0.94[EUR][1000 genomes]
rs2279149	0.94[EUR][1000 genomes]
rs2291004	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2303131	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28373708	0.93[EUR][1000 genomes]
rs28538699	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28605784	0.91[EUR][1000 genomes]
rs28623164	0.87[EUR][1000 genomes]
rs2891699	0.87[EUR][1000 genomes]
rs35540940	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35777021	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3760825	0.89[EUR][1000 genomes]
rs3803895	0.82[EUR][1000 genomes]
rs4801759	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4801803	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802766	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802889	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803195	0.89[EUR][1000 genomes]
rs4803460	0.82[EUR][1000 genomes]
rs4803539	0.82[EUR][1000 genomes]
rs59224125	0.91[EUR][1000 genomes]
rs6508732	0.97[EUR][1000 genomes]
rs6508733	0.97[EUR][1000 genomes]
rs713256	0.81[EUR][1000 genomes]
rs7246993	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7248733	0.93[EUR][1000 genomes]
rs7252099	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7252325	0.87[EUR][1000 genomes]
rs7252346	0.87[EUR][1000 genomes]
rs7253091	0.91[EUR][1000 genomes]
rs7253114	0.96[EUR][1000 genomes]
rs7255140	0.82[AMR][1000 genomes]
rs7255407	0.87[EUR][1000 genomes]
rs7255785	0.89[EUR][1000 genomes]
rs7255952	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7255972	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7255996	0.89[EUR][1000 genomes]
rs7256130	0.84[EUR][1000 genomes]
rs73631095	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106839	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109038	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109632	0.87[EUR][1000 genomes]
rs8112610	0.84[EUR][1000 genomes]
rs9676739	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9676967	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	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

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37998400-38004800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:37998600-38002400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:37998600-38002600	Weak transcription	Spleen	Spleen
4	chr19:37998600-38003200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:37998600-38003800	Weak transcription	Placenta	Placenta
6	chr19:37998600-38004200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:37998600-38004800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:37998600-38005200	Weak transcription	Psoas Muscle	Psoas
9	chr19:37998600-38008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr19:37998800-38002000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr19:37998800-38002000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:37998800-38002200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr19:37998800-38002200	Weak transcription	Aorta	Aorta
14	chr19:37998800-38002200	Weak transcription	Pancreas	Pancrea
15	chr19:37998800-38002400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:37998800-38002600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr19:37998800-38003800	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr19:37998800-38006200	Weak transcription	Esophagus	oesophagus
19	chr19:37998800-38010800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:37998800-38014000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr19:37998800-38021000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37998800-38022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:37999000-38002000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:37999000-38002000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:37999000-38002000	Weak transcription	Colon Smooth Muscle	Colon
26	chr19:37999000-38002000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr19:37999000-38002000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr19:37999000-38002200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:37999000-38002200	Weak transcription	Fetal Intestine Small	intestine
30	chr19:37999000-38002200	Weak transcription	Lung	lung
31	chr19:37999000-38002400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr19:37999000-38003800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr19:37999000-38004000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:37999000-38004200	Weak transcription	Brain Substantia Nigra	brain
35	chr19:37999000-38006800	Weak transcription	NH-A	brain
36	chr19:37999000-38007000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr19:37999000-38010800	Weak transcription	Right Ventricle	heart
38	chr19:37999000-38011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:37999000-38011400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:37999000-38013800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:37999200-38002000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr19:37999200-38002000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr19:37999200-38002200	Weak transcription	Brain Angular Gyrus	brain
45	chr19:37999200-38002400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr19:37999200-38002600	Weak transcription	Primary T cells from cord blood	blood
47	chr19:37999200-38003400	Weak transcription	Fetal Kidney	kidney
48	chr19:37999200-38003800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:37999200-38008000	Weak transcription	NHEK	skin
50	chr19:37999200-38008400	Weak transcription	Fetal Heart	heart

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