Variant report

Variant	rs2912406
Chromosome Location	chr19:37065732-37065733
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr19:37062890-37065821	SK-N-SH	brain:	n/a	n/a
2	CEBPB	chr19:37065711-37066009	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:37017989..37021035-chr19:37064029..37066517,3	MCF-7	breast:
2	chr19:36704361..36705921-chr19:37063810..37066277,2	K562	blood:
3	chr19:37038594..37041681-chr19:37063019..37065867,3	K562	blood:
4	chr19:36979379..36982047-chr19:37063909..37066157,2	K562	blood:
5	chr19:37062757..37066475-chr19:37067178..37075829,11	K562	blood:
6	chr19:37062757..37067111-chr19:37067178..37071986,8	K562	blood:
7	chr19:37017781..37019790-chr19:37064970..37066905,2	MCF-7	breast:
8	chr19:37065150..37067798-chr19:37072514..37074047,2	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092295.7.1-3	chr19:37065723-37065802	ENSG00000233527.4
2	lnc-AC092295.7.1-3	chr19:37065723-37065802	ENSG00000233527.4
3	lnc-AC092295.7.1-3	chr19:37065723-37065802	ENSG00000233527.4
4	lnc-AC092295.7.1-3	chr19:37065720-37065802	NONHSAT066015

No data

Variant related genes	Relation type
ENSG00000233527	TF binding region
ZNF529	TF binding region
ENSG00000267309	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10411411	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1053064	0.92[EUR][1000 genomes]
rs12162275	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12973307	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2912401	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912402	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912416	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2912417	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967424	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967455	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967470	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3096621	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3096626	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108169	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108170	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108175	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108180	0.89[EUR][1000 genomes]
rs3108198	0.88[EUR][1000 genomes]
rs3108199	0.86[EUR][1000 genomes]
rs3108200	0.88[EUR][1000 genomes]
rs3108207	0.92[EUR][1000 genomes]
rs3108213	0.88[EUR][1000 genomes]
rs3108547	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108548	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3108551	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108553	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3108554	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3108558	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3108561	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3108571	0.88[EUR][1000 genomes]
rs3108578	0.88[EUR][1000 genomes]
rs3108581	0.88[EUR][1000 genomes]
rs3108587	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3108595	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3108599	0.85[AFR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108601	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3108611	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3111543	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3111545	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111546	0.80[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71337534	0.83[EUR][1000 genomes]
rs7254978	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8112546	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	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
7	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription 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	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2912406	ZNF529	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37062800-37065800	Active TSS	HMEC	breast
2	chr19:37062800-37066000	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr19:37062800-37066000	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr19:37063000-37065800	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:37063000-37066000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:37063200-37065800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr19:37063200-37065800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:37063200-37065800	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:37063200-37065800	Active TSS	Right Ventricle	heart
10	chr19:37063400-37065800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:37063400-37065800	Active TSS	Fetal Intestine Large	intestine
12	chr19:37063400-37065800	Active TSS	Fetal Intestine Small	intestine
13	chr19:37063400-37065800	Active TSS	NHDF-Ad	bronchial
14	chr19:37063400-37066000	Active TSS	H1 Cell Line	embryonic stem cell
15	chr19:37063600-37065800	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:37063600-37065800	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr19:37063600-37066000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:37064600-37068800	ZNF genes & repeats	A549	lung
19	chr19:37064800-37065800	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr19:37064800-37065800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:37064800-37065800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:37064800-37066000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr19:37065000-37065800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:37065000-37065800	Flanking Active TSS	Liver	Liver
25	chr19:37065000-37065800	Flanking Active TSS	Brain Anterior Caudate	brain
26	chr19:37065000-37065800	Flanking Active TSS	Dnd41	blood
27	chr19:37065000-37066000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:37065000-37066000	Flanking Active TSS	Osteobl	bone
29	chr19:37065200-37065800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:37065200-37065800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr19:37065200-37065800	Flanking Active TSS	Hela-S3	cervix
32	chr19:37065200-37066000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr19:37065200-37066200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr19:37065200-37066200	Enhancers	Fetal Heart	heart
35	chr19:37065200-37067200	Weak transcription	Aorta	Aorta
36	chr19:37065200-37068000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:37065200-37068000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr19:37065400-37065800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:37065400-37065800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:37065400-37065800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr19:37065400-37065800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:37065400-37065800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr19:37065400-37065800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:37065400-37065800	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr19:37065400-37065800	Enhancers	Stomach Mucosa	stomach
46	chr19:37065400-37065800	Flanking Active TSS	NHEK	skin
47	chr19:37065400-37066000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr19:37065400-37066000	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr19:37065400-37066000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:37065400-37066000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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