Variant report

Variant	rs2562409
Chromosome Location	chr19:21601110-21601111
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	chr19:21596819..21599115-chr19:21600673..21603133,2	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1114305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1875256	0.84[EUR][1000 genomes]
rs2086319	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2434996	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2562402	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2562415	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2562438	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2650797	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2650798	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2650842	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2650849	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2650851	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs279804	0.85[EUR][1000 genomes]
rs279805	0.85[EUR][1000 genomes]
rs279810	0.85[EUR][1000 genomes]
rs279811	0.85[EUR][1000 genomes]
rs279812	0.85[EUR][1000 genomes]
rs279814	0.85[EUR][1000 genomes]
rs279815	0.85[EUR][1000 genomes]
rs279816	0.85[EUR][1000 genomes]
rs279819	0.82[EUR][1000 genomes]
rs279820	0.85[EUR][1000 genomes]
rs2914626	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2914627	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2914635	0.86[AMR][1000 genomes]
rs2914645	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928188	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2928209	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2928216	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2928218	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2937157	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2937174	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2968022	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968023	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968024	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2968040	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2968041	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2968045	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2968046	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968066	0.92[EUR][1000 genomes]
rs2968082	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968086	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs472472	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs475162	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs476376	0.85[EUR][1000 genomes]
rs478046	0.85[EUR][1000 genomes]
rs487991	0.92[EUR][1000 genomes]
rs489613	0.88[AMR][1000 genomes]
rs489845	0.92[EUR][1000 genomes]
rs492271	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs499445	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs501563	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs504026	0.85[EUR][1000 genomes]
rs508656	0.85[EUR][1000 genomes]
rs511469	0.85[EUR][1000 genomes]
rs527060	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs537114	0.85[EUR][1000 genomes]
rs540637	0.85[EUR][1000 genomes]
rs540714	0.85[EUR][1000 genomes]
rs541639	0.85[EUR][1000 genomes]
rs547516	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs555596	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs583680	0.85[EUR][1000 genomes]
rs586144	0.86[EUR][1000 genomes]
rs598959	0.92[EUR][1000 genomes]
rs600186	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs609806	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs612877	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs631436	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs651454	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs661453	0.85[EUR][1000 genomes]
rs8102235	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8112775	0.92[EUR][1000 genomes]
rs924485	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv911420	chr19:21454672-21613397	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	esv1793996	chr19:21544242-21609607	Active TSS Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	esv1801985	chr19:21544242-21609607	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	esv1844586	chr19:21544242-21609607	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv1834499	chr19:21557835-21609607	Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1834993	chr19:21557835-21609607	Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv911421	chr19:21579718-21613397	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
15	nsv578953	chr19:21586797-21609607	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
16	nsv578954	chr19:21587261-21604510	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21580600-21602400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:21581600-21601800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr19:21581800-21607000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:21585000-21614000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:21590200-21606400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:21590600-21608200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
7	chr19:21590800-21601200	Strong transcription	Ovary	ovary
8	chr19:21591800-21607000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
9	chr19:21592800-21601200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr19:21593200-21602400	Weak transcription	HSMM	muscle
11	chr19:21593400-21610200	ZNF genes & repeats	Liver	Liver
12	chr19:21593600-21606600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr19:21594200-21601200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr19:21595000-21601400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:21595400-21601200	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr19:21595400-21601400	Strong transcription	Fetal Intestine Large	intestine
17	chr19:21596800-21601200	Weak transcription	Fetal Muscle Leg	muscle
18	chr19:21597000-21601200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:21597000-21602200	Weak transcription	HSMMtube	muscle
20	chr19:21597200-21601200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:21597200-21601800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:21597200-21602400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr19:21597600-21602400	Weak transcription	Right Ventricle	heart
24	chr19:21597800-21601200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr19:21597800-21601800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:21598000-21602000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:21598200-21601400	Strong transcription	Brain Hippocampus Middle	brain
28	chr19:21598400-21601600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:21598600-21602200	Weak transcription	Brain Anterior Caudate	brain
30	chr19:21598600-21603600	Weak transcription	Fetal Kidney	kidney
31	chr19:21598600-21605800	Weak transcription	Colon Smooth Muscle	Colon
32	chr19:21599200-21601600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr19:21599200-21601800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr19:21599400-21601400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
35	chr19:21599400-21603000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
36	chr19:21599400-21603200	ZNF genes & repeats	Fetal Brain Female	brain
37	chr19:21599600-21601200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr19:21599600-21601200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:21599600-21601200	Strong transcription	Fetal Stomach	stomach
40	chr19:21599600-21601600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:21599600-21601800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
42	chr19:21599600-21602800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:21599600-21603000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:21599600-21603000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:21599600-21603000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr19:21599600-21603800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
47	chr19:21599600-21605200	ZNF genes & repeats	Fetal Intestine Small	intestine
48	chr19:21599600-21611000	ZNF genes & repeats	Adipose Nuclei	Adipose
49	chr19:21599800-21601400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr19:21599800-21606400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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