Variant report

Variant	rs329973
Chromosome Location	chr19:53105547-53105548
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:53105140-53105831	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:53105160-53105552	K562	blood:	n/a	n/a
3	CTCF	chr19:53105254-53105566	GM12878	blood:	n/a	n/a
4	RAD21	chr19:53105214-53105550	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr19:53105209-53105555	IMR90	lung:	n/a	n/a
6	ZNF263	chr19:53105307-53105814	HEK293-T-REx	kidney:	n/a	chr19:53105487-53105508 chr19:53105426-53105435
7	POLR2A	chr19:53105364-53105590	GM12878	blood:	n/a	n/a
8	MAZ	chr19:53103821-53106145	IMR90	lung:	n/a	chr19:53104498-53104508 chr19:53104431-53104441
9	HEY1	chr19:53105202-53105652	K562	blood:	n/a	n/a
10	CTCF	chr19:53105400-53105550	RPTEC	kidney:	n/a	n/a
11	POLR2A	chr19:53105224-53105625	GM12892	blood:	n/a	n/a
12	CTCF	chr19:53105360-53105590	SAEC	small airway:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52771721..52774334-chr19:53104602..53106334,2	MCF-7	breast:
2	chr19:53105509..53107487-chr19:53113900..53115997,2	K562	blood:
3	chr19:53030382..53031999-chr19:53102744..53106373,4	K562	blood:
4	chr19:53100001..53102540-chr19:53104328..53106583,2	MCF-7	breast:
5	chr19:53103475..53106137-chr19:53106571..53108256,2	K562	blood:
6	chr19:53091479..53093203-chr19:53104357..53107211,2	MCF-7	breast:
7	chr19:53104394..53106484-chr19:53154672..53157186,2	K562	blood:
8	chr19:53100919..53102551-chr19:53104466..53106179,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268970	TF binding region
ENSG00000196214	Chromatin interaction
ENSG00000123870	Chromatin interaction
ENSG00000268970	Chromatin interaction
ENSG00000269825	Chromatin interaction
ENSG00000198482	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10401627	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11882556	0.85[EUR][1000 genomes]
rs4801922	0.87[CEU][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4802976	0.85[EUR][1000 genomes]
rs7254868	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs7260122	0.84[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8106002	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057296	chr19:52950339-53396986	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1065584	chr19:53043126-53127459	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv833874	chr19:53058014-53257875	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv458743	chr19:53065661-53114267	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription 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	9 gene(s)	inside rSNPs	diseases
5	nsv580027	chr19:53065661-53114267	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	9 gene(s)	inside rSNPs	diseases
6	nsv912304	chr19:53071155-53114267	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv912305	chr19:53092465-53349850	Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv912306	chr19:53092465-53400760	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv912307	chr19:53092465-53433054	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Genic enhancers 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 target site	32 gene(s)	inside rSNPs	diseases
10	nsv912308	chr19:53092465-53436337	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv912309	chr19:53092465-53440653	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
12	nsv912310	chr19:53092465-53451291	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv828616	chr19:53095216-53137823	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv912311	chr19:53103875-53212361	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv912312	chr19:53103875-53296371	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv912313	chr19:53103875-53436337	ZNF genes & repeats Weak transcription Strong transcription Active TSS 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	30 gene(s)	inside rSNPs	diseases
17	nsv912314	chr19:53105547-53144082	Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
18	nsv912315	chr19:53105547-53149967	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
19	nsv912316	chr19:53105547-53158023	Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
20	nsv912317	chr19:53105547-53440653	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs329973	NLRP8	cis	cerebellum	SCAN
rs329973	ZSCAN18	cis	cerebellum	SCAN
rs329973	BRSK1	cis	parietal	SCAN
rs329973	LILRB5	cis	parietal	SCAN
rs329973	ZNF542	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53103400-53105600	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr19:53103600-53105600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr19:53103600-53105800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:53103800-53105600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:53103800-53105600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:53103800-53105600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:53103800-53105600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:53103800-53105600	Active TSS	Fetal Kidney	kidney
9	chr19:53103800-53105600	Active TSS	GM12878-XiMat	blood
10	chr19:53104000-53105600	Active TSS	Fetal Intestine Large	intestine
11	chr19:53104000-53105600	Active TSS	HepG2	liver
12	chr19:53104000-53105800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr19:53104000-53106000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:53104000-53106000	Active TSS	Fetal Intestine Small	intestine
15	chr19:53104000-53106200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:53104200-53105600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:53104200-53105600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:53104200-53105600	Active TSS	Thymus	Thymus
19	chr19:53104200-53105800	Active TSS	Rectal Smooth Muscle	rectum
20	chr19:53104600-53105600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:53104600-53105600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr19:53104600-53105600	Flanking Active TSS	HMEC	breast
23	chr19:53104600-53105800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:53104800-53105600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
25	chr19:53104800-53105600	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr19:53104800-53105600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:53104800-53105600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:53104800-53105600	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr19:53104800-53105800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr19:53104800-53105800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:53105000-53105600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr19:53105000-53105600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:53105000-53105600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr19:53105000-53105600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:53105000-53105600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr19:53105000-53105600	Flanking Active TSS	Gastric	stomach
37	chr19:53105000-53105600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
38	chr19:53105000-53105600	Flanking Active TSS	Osteobl	bone
39	chr19:53105000-53105800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr19:53105000-53105800	Flanking Active TSS	Dnd41	blood
41	chr19:53105000-53105800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr19:53105000-53115800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr19:53105200-53105600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:53105200-53105600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:53105200-53105600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr19:53105200-53105600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr19:53105200-53105600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:53105200-53105600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:53105200-53105600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:53105200-53105600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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