Variant report

Variant	rs2060238
Chromosome Location	chr19:19999159-19999160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:19999111-19999161	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000265339	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10406883	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11786	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11881376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16994693	0.80[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098331	1.00[ASN][1000 genomes]
rs2335372	1.00[ASN][1000 genomes]
rs55696844	1.00[ASN][1000 genomes]
rs55849911	1.00[ASN][1000 genomes]
rs55984158	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57088108	1.00[ASN][1000 genomes]
rs57575150	1.00[ASN][1000 genomes]
rs57920747	1.00[ASN][1000 genomes]
rs58922627	0.86[ASN][1000 genomes]
rs58948242	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59511604	1.00[ASN][1000 genomes]
rs59795312	0.93[EUR][1000 genomes]
rs60409469	1.00[ASN][1000 genomes]
rs60588790	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249318	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251285	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253023	1.00[ASN][1000 genomes]
rs7254824	1.00[ASN][1000 genomes]
rs73530903	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530906	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530911	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530927	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530932	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530989	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73530999	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73925530	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73925536	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73925537	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104442	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv911314	chr19:19866371-20021046	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv911315	chr19:19872093-20021046	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv911316	chr19:19890450-20021046	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv961192	chr19:19906394-20083740	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
8	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
9	esv3413756	chr19:19936066-20072059	ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	esv3380276	chr19:19936583-20073601	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1066792	chr19:19940585-20000701	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3429980	chr19:19943721-20102072	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic 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	15 gene(s)	inside rSNPs	diseases
13	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
14	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
15	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
16	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic 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	23 gene(s)	inside rSNPs	diseases
17	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers 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	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19977600-20006800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:19978800-20007600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:19979000-20004000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:19979200-20007400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:19979400-20008200	ZNF genes & repeats	Liver	Liver
6	chr19:19980200-20001000	Weak transcription	Fetal Heart	heart
7	chr19:19982400-20000200	Weak transcription	Gastric	stomach
8	chr19:19984200-19999400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:19986800-20004800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:19988000-20001400	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:19988600-20003800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:19989600-20007400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:19990800-20007000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:19991000-19999800	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr19:19991000-20006200	ZNF genes & repeats	Brain Germinal Matrix	brain
16	chr19:19991800-20005600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:19992200-20006200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr19:19993400-20000400	Weak transcription	Brain Angular Gyrus	brain
19	chr19:19993400-20001800	Weak transcription	HSMM	muscle
20	chr19:19994600-20002000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr19:19994800-20007600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:19995000-20006800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
23	chr19:19995600-20000200	Weak transcription	Left Ventricle	heart
24	chr19:19995600-20000200	Weak transcription	Pancreas	Pancrea
25	chr19:19995600-20000600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr19:19995600-20004000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:19996200-20003600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
28	chr19:19996600-20000600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:19996600-20003400	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr19:19996600-20004000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr19:19996600-20004200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:19996600-20005400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
33	chr19:19996600-20005400	ZNF genes & repeats	Dnd41	blood
34	chr19:19996600-20005400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
35	chr19:19996800-19999200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:19996800-19999200	ZNF genes & repeats	Aorta	Aorta
37	chr19:19996800-19999200	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr19:19996800-20002000	ZNF genes & repeats	Fetal Intestine Large	intestine
39	chr19:19996800-20003400	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr19:19996800-20004000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr19:19996800-20004800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:19996800-20006400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
43	chr19:19997000-20001000	Weak transcription	Osteobl	bone
44	chr19:19997400-20000400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:19997400-20000400	Weak transcription	NH-A	brain
46	chr19:19997400-20001000	Weak transcription	Brain Cingulate Gyrus	brain
47	chr19:19997400-20002200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:19997600-19999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr19:19998000-19999200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr19:19998000-19999200	ZNF genes & repeats	Fetal Stomach	stomach

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