Variant report

Variant	rs1644646
Chromosome Location	chr19:37463802-37463803
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	chr19:37463700-37464602	PANC-1	pancreas:	n/a	n/a
2	RAD21	chr19:37463702-37465035	SK-N-SH	brain:	n/a	chr19:37464972-37464982 chr19:37464403-37464415 chr19:37464202-37464214 chr19:37464398-37464417 chr19:37464053-37464063 chr19:37464403-37464413 chr19:37464013-37464026
3	GABPA	chr19:37463645-37464599	MCF-7	breast:	n/a	n/a
4	POLR2A	chr19:37463760-37464649	ProgFib	skin:	n/a	n/a
5	GABPA	chr19:37463780-37464554	MCF-7	breast:	n/a	n/a
6	CTCF	chr19:37463780-37463930	HRE	kidney:	n/a	n/a
7	CTCF	chr19:37463699-37465010	SK-N-SH	brain:	n/a	chr19:37464018-37464027 chr19:37464014-37464027
8	POLR2A	chr19:37463797-37464604	PANC-1	pancreas:	n/a	n/a
9	CTCF	chr19:37463680-37463830	NHDF-neo	bronchial:	n/a	n/a
10	SIN3AK20	chr19:37463765-37464790	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:37463749-37464511	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIX5	chr19:37463802-37464245	H1-hESC	embryonic stem cell:	n/a	chr19:37464043-37464052 chr19:37464045-37464054 chr19:37464041-37464055

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37463031..37465781-chr19:37707432..37709239,2	MCF-7	breast:

Variant related genes	Relation type
ZNF568	TF binding region
ENSG00000245680	Chromatin interaction
ENSG00000188283	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1069756	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1069757	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1644644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1644653	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1644655	0.94[AFR][1000 genomes]
rs1644680	0.94[AFR][1000 genomes]
rs1644694	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1644703	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1644709	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1667332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1667334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1667361	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1667362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2254217	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2435066	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562584	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562586	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562588	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2562590	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35624635	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs477893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs485980	0.91[AFR][1000 genomes]
rs486891	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs549031	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs569068	0.88[AFR][1000 genomes]
rs573596	0.94[AFR][1000 genomes]
rs577844	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs703528	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs703529	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs703532	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs703533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs703534	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs703536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7250855	1.00[AMR][1000 genomes]
rs7251397	1.00[AMR][1000 genomes]
rs7251690	1.00[AMR][1000 genomes]
rs7255103	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7255177	1.00[AMR][1000 genomes]
rs7255728	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7257279	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7258653	1.00[AMR][1000 genomes]
rs7259422	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7259881	1.00[AMR][1000 genomes]
rs8102364	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs826286	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs826287	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs862248	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	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
6	nsv521605	chr19:37261810-37483444	ZNF genes & repeats Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
9	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers 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 target site	25 gene(s)	inside rSNPs	diseases
11	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv523848	chr19:37357289-37487632	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
14	nsv833818	chr19:37427808-37602800	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
15	nsv579463	chr19:37437106-37488055	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS 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 target site	17 gene(s)	inside rSNPs	diseases
17	esv1828064	chr19:37463270-37467305	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
18	esv1808096	chr19:37463582-37464848	Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37463200-37464000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr19:37463200-37464000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:37463200-37464000	Flanking Active TSS	Dnd41	blood
4	chr19:37463200-37464200	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr19:37463200-37464200	Active TSS	Colonic Mucosa	Colon
6	chr19:37463200-37464600	Active TSS	Brain Angular Gyrus	brain
7	chr19:37463200-37464600	Active TSS	Brain Anterior Caudate	brain
8	chr19:37463200-37464600	Active TSS	Brain Cingulate Gyrus	brain
9	chr19:37463200-37464600	Active TSS	Placenta Amnion	Placenta Amnion
10	chr19:37463200-37464600	Active TSS	NHEK	skin
11	chr19:37463200-37464800	Active TSS	Fetal Intestine Small	intestine
12	chr19:37463200-37465000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:37463200-37465000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr19:37463200-37465200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
15	chr19:37463200-37465200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
16	chr19:37463400-37464000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
17	chr19:37463400-37464000	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr19:37463400-37464000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
19	chr19:37463400-37464000	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr19:37463400-37464000	Flanking Active TSS	Placenta	Placenta
21	chr19:37463400-37464400	Active TSS	Brain Hippocampus Middle	brain
22	chr19:37463400-37464400	ZNF genes & repeats	Fetal Thymus	thymus
23	chr19:37463400-37464400	Active TSS	Rectal Mucosa Donor 31	rectum
24	chr19:37463400-37464600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr19:37463400-37464600	Active TSS	Primary T cells from cord blood	blood
26	chr19:37463400-37464600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:37463400-37464600	Active TSS	Psoas Muscle	Psoas
28	chr19:37463400-37464600	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:37463400-37464600	Active TSS	Right Atrium	heart
30	chr19:37463400-37464800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:37463400-37464800	Active TSS	HSMMtube	muscle
32	chr19:37463400-37465000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:37463400-37465000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:37463400-37465000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr19:37463400-37465000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:37463400-37465000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:37463400-37465000	Active TSS	Fetal Intestine Large	intestine
38	chr19:37463400-37465000	Active TSS	Osteobl	bone
39	chr19:37463400-37465200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:37463400-37465200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:37463400-37465200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:37463400-37465200	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr19:37463400-37465200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr19:37463400-37465200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:37463400-37465200	ZNF genes & repeats	Lung	lung
46	chr19:37463400-37465400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
47	chr19:37463400-37465400	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr19:37463600-37464000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:37463600-37464000	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr19:37463600-37464000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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