Variant report

Variant	rs73560806
Chromosome Location	chr19:42028778-42028779
allele	A/G
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	chr19:42027718-42028803	GM18505	blood:	n/a	n/a
2	SUZ12	chr19:42027521-42029339	NT2-D1	testis:	n/a	n/a
3	POLR2A	chr19:42028237-42028845	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr19:42027675-42028800	GM12878	blood:	n/a	n/a
5	HEY1	chr19:42028434-42028785	HepG2	liver:	n/a	chr19:42028676-42028691
6	POLR2A	chr19:42027889-42028812	GM19193	blood:	n/a	n/a
7	POU2F2	chr19:42028437-42028811	GM12891	blood:	n/a	n/a
8	TAF1	chr19:42028427-42028779	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:42027599-42028845	GM12892	blood:	n/a	n/a
10	POLR2A	chr19:42028450-42028807	GM12878	blood:	n/a	n/a
11	PAX5	chr19:42028300-42028812	GM12878	blood:	n/a	n/a
12	TAF1	chr19:42028339-42028827	GM12878	blood:	n/a	n/a
13	BHLHE40	chr19:42028460-42028816	GM12878	blood:	n/a	chr19:42028587-42028603 chr19:42028585-42028601
14	POLR2A	chr19:42027671-42028849	GM12892	blood:	n/a	n/a
15	POLR2A	chr19:42028463-42028828	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:42027676-42028797	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:42028400-42028802	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:42028251-42028803	GM12891	blood:	n/a	n/a
19	RUNX3	chr19:42028165-42028788	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:42028424-42028783	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
PLEKHA3P1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10406890	1.00[AMR][1000 genomes]
rs10414658	1.00[AMR][1000 genomes]
rs10418236	1.00[AMR][1000 genomes]
rs10425322	1.00[AMR][1000 genomes]
rs16975289	1.00[AMR][1000 genomes]
rs73558643	1.00[AMR][1000 genomes]
rs73558647	1.00[AMR][1000 genomes]
rs73558696	1.00[AMR][1000 genomes]
rs73558697	1.00[AMR][1000 genomes]
rs73558700	1.00[AMR][1000 genomes]
rs73560816	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73560817	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73560837	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510767	chr19:41962486-42049165	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv911770	chr19:41962486-42066279	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv911771	chr19:41962486-42085873	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1055515	chr19:41968797-42057334	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv911772	chr19:41985624-42066279	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911773	chr19:42001210-42085873	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv579601	chr19:42006714-42031592	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription	TF binding region CpG island	3 gene(s)	inside rSNPs	diseases
8	nsv579602	chr19:42015468-42047924	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42027200-42029400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr19:42027400-42029200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr19:42027600-42028800	Flanking Active TSS	Primary B cells from peripheral blood	blood
4	chr19:42027600-42028800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
5	chr19:42027600-42029000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:42027600-42029000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr19:42027800-42028800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr19:42027800-42028800	Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr19:42027800-42028800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:42027800-42028800	Active TSS	GM12878-XiMat	blood
11	chr19:42027800-42029000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:42027800-42029000	Active TSS	Right Atrium	heart
13	chr19:42027800-42029000	Bivalent/Poised TSS	Thymus	Thymus
14	chr19:42028000-42028800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:42028000-42028800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
16	chr19:42028000-42028800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:42028000-42028800	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr19:42028000-42028800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr19:42028000-42028800	Active TSS	Primary T killer memory cells from peripheral blood	blood
20	chr19:42028000-42029000	Bivalent/Poised TSS	A549	lung
21	chr19:42028200-42028800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:42028200-42028800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:42028200-42028800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
24	chr19:42028200-42028800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:42028200-42028800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
26	chr19:42028200-42028800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
27	chr19:42028200-42028800	Bivalent Enhancer	Fetal Brain Male	brain
28	chr19:42028200-42028800	Bivalent/Poised TSS	Left Ventricle	heart
29	chr19:42028200-42028800	Active TSS	Right Ventricle	heart
30	chr19:42028200-42028800	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
31	chr19:42028200-42029000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:42028200-42029000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr19:42028200-42029000	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr19:42028200-42029000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:42028400-42028800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
36	chr19:42028400-42028800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:42028400-42028800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
38	chr19:42028400-42028800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:42028400-42028800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:42028400-42028800	Active TSS	Primary T cells from cord blood	blood
41	chr19:42028400-42028800	Active TSS	Primary T cells fromperipheralblood	blood
42	chr19:42028400-42028800	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr19:42028400-42028800	Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr19:42028400-42028800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:42028400-42028800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:42028400-42028800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:42028400-42028800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:42028400-42028800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:42028400-42028800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:42028400-42028800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin

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