Variant report

Variant	rs1391581
Chromosome Location	chr19:22715257-22715258
allele	A/C
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	CTCF	chr19:22715180-22715330	HEK293	kidney:	n/a	n/a
2	CTCF	chr19:22715242-22715334	Kidney_OC	kidney:	n/a	n/a
3	POLR2A	chr19:22715209-22715447	MCF-7	breast:	n/a	n/a
4	CTCF	chr19:22715250-22715331	Pancreas_OC	pancreas:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF98-9	chr19:22715141-22715368	NONHSAT063793
2	lnc-ZNF98-9	chr19:22715141-22715287	NONHSAT063787

Variant related genes	Relation type
ENSG00000260599	TF binding region
ENSG00000269364	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2915923	0.82[CEU][hapmap]
rs2957838	0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3360126	chr19:22209871-23199213	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	esv3333410	chr19:22213338-23199725	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv525240	chr19:22250912-23216667	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
4	esv3363663	chr19:22320301-23103053	Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv911439	chr19:22325391-22820798	ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv911440	chr19:22325391-23216667	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv819194	chr19:22336264-23223696	ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
8	nsv911442	chr19:22338142-22801310	Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv911443	chr19:22338142-22899585	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
10	nsv911444	chr19:22338142-23198437	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
11	nsv911445	chr19:22346403-22899585	Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
12	nsv819205	chr19:22346403-23199700	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
13	nsv1064071	chr19:22359491-23153773	Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
14	nsv543957	chr19:22359491-23153773	Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
15	nsv932157	chr19:22359492-23192975	Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
16	esv3387241	chr19:22383621-23175441	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
17	nsv1059925	chr19:22408435-23083293	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
18	nsv1056393	chr19:22408435-23106126	Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
19	nsv911448	chr19:22622753-22799293	Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	esv3496801	chr19:22635989-23028182	Enhancers ZNF genes & repeats Active TSS Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
21	esv3496802	chr19:22635989-23028182	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
22	nsv833787	chr19:22639018-22812145	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
23	esv3529242	chr19:22650256-22863256	Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
24	esv3529243	chr19:22650256-22863256	Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
25	nsv1060550	chr19:22675311-22811229	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island lncRNA	18 gene(s)	inside rSNPs	diseases
26	nsv9681	chr19:22708724-22716078	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv578977	chr19:22713581-22736251	ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1391581	RFXANK	cis	cerebellum	SCAN
rs1391581	HAPLN4	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:22708600-22716200	Active TSS	Ovary	ovary
2	chr19:22709600-22716200	Active TSS	Aorta	Aorta
3	chr19:22711800-22716200	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:22714400-22715400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr19:22714400-22716000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr19:22714400-22716200	Active TSS	Pancreas	Pancrea
7	chr19:22714600-22715600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:22714600-22716000	Active TSS	Brain Angular Gyrus	brain
9	chr19:22714600-22716000	Active TSS	Brain Anterior Caudate	brain
10	chr19:22714600-22716000	Active TSS	Brain Hippocampus Middle	brain
11	chr19:22714600-22716000	Active TSS	Right Atrium	heart
12	chr19:22714800-22715400	Active TSS	Right Ventricle	heart
13	chr19:22714800-22715800	Active TSS	Colonic Mucosa	Colon
14	chr19:22714800-22715800	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr19:22714800-22716000	Active TSS	Brain Cingulate Gyrus	brain
16	chr19:22714800-22716000	Active TSS	Brain Substantia Nigra	brain
17	chr19:22714800-22716000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
18	chr19:22714800-22716000	Active TSS	Fetal Kidney	kidney
19	chr19:22714800-22716000	Active TSS	Fetal Muscle Trunk	muscle
20	chr19:22714800-22716000	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr19:22714800-22716000	Active TSS	Rectal Smooth Muscle	rectum
22	chr19:22714800-22716200	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr19:22714800-22716200	ZNF genes & repeats	Fetal Stomach	stomach
24	chr19:22715000-22715400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:22715000-22715400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
26	chr19:22715000-22715400	Bivalent Enhancer	Lung	lung
27	chr19:22715000-22715400	Enhancers	Psoas Muscle	Psoas
28	chr19:22715000-22715800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
29	chr19:22715000-22716000	Bivalent/Poised TSS	Left Ventricle	heart
30	chr19:22715000-22716000	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
31	chr19:22715000-22716200	Active TSS	Colon Smooth Muscle	Colon
32	chr19:22715200-22715400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr19:22715200-22716000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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