Variant report

Variant	rs16983728
Chromosome Location	chr19:52839110-52839111
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	GABPA	chr19:52839104-52839983	MCF-7	breast:	n/a	chr19:52839477-52839491 chr19:52839785-52839792 chr19:52839474-52839488
2	POLR2A	chr19:52839107-52840563	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:52839015-52839920	HUVEC	blood vessel:	n/a	n/a
4	PML	chr19:52839102-52839908	GM12878	blood:	n/a	n/a
5	ELF1	chr19:52839034-52839882	MCF-7	breast:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
6	POLR2A	chr19:52839105-52839837	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:52839066-52840245	HL-60	blood:	n/a	n/a
8	SIN3AK20	chr19:52839063-52839903	MCF-7	breast:	n/a	n/a
9	MXI1	chr19:52838760-52840879	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr19:52839108-52839879	MCF-7	breast:	n/a	n/a
11	POLR2A	chr19:52839085-52839885	SK-N-SH	brain:	n/a	n/a
12	REST	chr19:52838918-52840640	H1-neurons	neurons:	n/a	chr19:52839580-52839590 chr19:52839635-52839648 chr19:52840483-52840496
13	ELF1	chr19:52839098-52840140	GM12878	blood:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
14	ELF1	chr19:52839012-52839932	SK-N-SH	brain:	n/a	chr19:52839500-52839509 chr19:52839499-52839510 chr19:52839501-52839510
15	POLR2A	chr19:52839055-52839937	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52771880..52774244-chr19:52838831..52841718,3	MCF-7	breast:
2	chr19:52771196..52774040-chr19:52836837..52839956,3	MCF-7	breast:
3	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:
4	chr19:52641710..52644473-chr19:52838292..52841252,2	MCF-7	breast:

Variant related genes	Relation type
ZNF610	TF binding region
ENSG00000204611	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000198464	Chromatin interaction
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs62108271	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6509631	0.92[EUR][1000 genomes]
rs7249361	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7253555	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS 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 miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS 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 miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv458742	chr19:52808986-52866171	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
9	nsv580008	chr19:52808986-52866171	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
10	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription 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	16 gene(s)	inside rSNPs	diseases
11	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers 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	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52802400-52841800	ZNF genes & repeats	Liver	Liver
2	chr19:52833000-52839400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:52838600-52839200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
4	chr19:52838600-52839200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
5	chr19:52838600-52839400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:52838600-52839400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
7	chr19:52838600-52839400	ZNF genes & repeats	Thymus	Thymus
8	chr19:52838600-52839400	Flanking Active TSS	Dnd41	blood
9	chr19:52838600-52839400	ZNF genes & repeats	NHLF	lung
10	chr19:52838600-52839600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:52838600-52839600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
12	chr19:52838600-52839600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
13	chr19:52838600-52839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr19:52838600-52839600	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr19:52838600-52840000	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr19:52838600-52840200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr19:52838600-52840400	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr19:52838600-52840600	ZNF genes & repeats	Pancreas	Pancrea
19	chr19:52838600-52840600	ZNF genes & repeats	Spleen	Spleen
20	chr19:52838600-52840800	Active TSS	iPS-18 Cell Line	embryonic stem cell
21	chr19:52838600-52840800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:52838600-52840800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr19:52838800-52839200	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr19:52838800-52839200	ZNF genes & repeats	Colon Smooth Muscle	Colon
25	chr19:52838800-52839200	ZNF genes & repeats	Fetal Heart	heart
26	chr19:52838800-52839400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
27	chr19:52838800-52839400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
28	chr19:52838800-52839400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:52838800-52839400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr19:52838800-52839400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:52838800-52839400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:52838800-52839400	ZNF genes & repeats	Fetal Intestine Small	intestine
33	chr19:52838800-52839400	ZNF genes & repeats	Fetal Thymus	thymus
34	chr19:52838800-52839400	ZNF genes & repeats	HSMM	muscle
35	chr19:52838800-52839600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:52838800-52839600	Active TSS	Brain Germinal Matrix	brain
37	chr19:52838800-52839800	Active TSS	Primary hematopoietic stem cells	blood
38	chr19:52838800-52840000	Active TSS	Brain Angular Gyrus	brain
39	chr19:52838800-52840000	Active TSS	Brain Anterior Caudate	brain
40	chr19:52838800-52840000	Active TSS	Brain Hippocampus Middle	brain
41	chr19:52838800-52840000	Active TSS	Rectal Smooth Muscle	rectum
42	chr19:52838800-52840200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:52838800-52840200	Active TSS	Primary T cells from cord blood	blood
44	chr19:52838800-52840200	Active TSS	Brain Cingulate Gyrus	brain
45	chr19:52838800-52840200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:52838800-52840400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:52838800-52840400	Active TSS	Fetal Brain Female	brain
48	chr19:52838800-52840400	Active TSS	Psoas Muscle	Psoas
49	chr19:52838800-52840400	ZNF genes & repeats	GM12878-XiMat	blood
50	chr19:52838800-52840800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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