Variant report

Variant	rs4254438
Chromosome Location	chr19:18395537-18395538
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	POLR2A	chr19:18395495-18396062	GM12891	blood:	n/a	n/a
2	PML	chr19:18395370-18396078	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:18395490-18396127	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:18395486-18395906	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:18395515-18395944	GM12892	blood:	n/a	n/a
6	POLR2A	chr19:18395531-18395752	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZEB1	chr19:18395464-18395947	GM12878	blood:	n/a	chr19:18395867-18395874 chr19:18395497-18395508
8	POLR2A	chr19:18395509-18396033	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:18395443-18395600	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr19:18395365-18396260	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18260692..18269532-chr19:18383927..18395911,19	K562	blood:
2	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:

Variant related genes	Relation type
JUND	TF binding region
ENSG00000105647	Chromatin interaction
ENSG00000269145	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000268173	Chromatin interaction
ENSG00000130511	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10416600	0.80[YRI][hapmap]
rs12462798	0.82[ASN][1000 genomes]
rs12608504	0.86[YRI][hapmap]
rs1549142	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2384991	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2384992	0.87[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2384993	0.84[ASN][1000 genomes]
rs41523455	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4378729	0.85[ASN][1000 genomes]
rs4531856	0.82[YRI][hapmap]
rs7249	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8109936	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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 miRNA	162 gene(s)	inside rSNPs	diseases
6	nsv911268	chr19:18351674-18395537	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
7	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
9	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
10	nsv828472	chr19:18377725-18404131	Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
11	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
12	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
13	esv1793726	chr19:18381600-18400786	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	104 gene(s)	inside rSNPs	diseases
14	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
15	esv1801478	chr19:18391070-18395537	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4254438	ZNF714	cis	parietal	SCAN
rs4254438	ZNF429	cis	parietal	SCAN
rs4254438	GATAD2A	cis	cerebellum	SCAN
rs4254438	KIAA1683	cis	cerebellum	SCAN
rs4254438	ZNF714	cis	cerebellum	SCAN
rs4254438	USE1	cis	cerebellum	SCAN
rs4254438	ZNF506	cis	cerebellum	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18393600-18395600	Weak transcription	Small Intestine	intestine
2	chr19:18393800-18395600	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr19:18393800-18395600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr19:18393800-18396400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:18393800-18396800	Weak transcription	Ovary	ovary
6	chr19:18393800-18397400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr19:18393800-18397400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr19:18393800-18397400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr19:18393800-18397400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:18393800-18397400	Weak transcription	Esophagus	oesophagus
11	chr19:18393800-18397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:18393800-18397800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:18393800-18398000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:18393800-18398000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr19:18393800-18398400	Weak transcription	NH-A	brain
16	chr19:18393800-18399000	Weak transcription	Fetal Kidney	kidney
17	chr19:18393800-18401000	Weak transcription	Thymus	Thymus
18	chr19:18393800-18401200	Weak transcription	Right Atrium	heart
19	chr19:18393800-18402000	Weak transcription	Aorta	Aorta
20	chr19:18394000-18395600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr19:18394000-18395600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:18394000-18395600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr19:18394000-18395600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr19:18394000-18395600	Weak transcription	Lung	lung
25	chr19:18394000-18395600	Weak transcription	Stomach Mucosa	stomach
26	chr19:18394000-18395600	Weak transcription	HMEC	breast
27	chr19:18394000-18395600	Weak transcription	Osteobl	bone
28	chr19:18394000-18396000	Weak transcription	NHLF	lung
29	chr19:18394000-18396400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr19:18394000-18396800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:18394000-18396800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr19:18394000-18396800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:18394000-18396800	Weak transcription	HSMMtube	muscle
34	chr19:18394000-18396800	Weak transcription	NHDF-Ad	bronchial
35	chr19:18394000-18397000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr19:18394000-18397200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr19:18394000-18397200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:18394000-18397400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:18394000-18397400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr19:18394000-18397400	Weak transcription	Hela-S3	cervix
41	chr19:18394000-18397400	Weak transcription	HSMM	muscle
42	chr19:18394000-18398800	Weak transcription	Fetal Lung	lung
43	chr19:18394000-18398800	Weak transcription	A549	lung
44	chr19:18394000-18400400	Weak transcription	Dnd41	blood
45	chr19:18394000-18400600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:18394000-18400800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:18394000-18401200	Weak transcription	Brain Hippocampus Middle	brain
48	chr19:18394000-18401400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr19:18394000-18401400	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:18394000-18402000	Weak transcription	Brain Anterior Caudate	brain

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