Variant report

Variant	rs1529717
Chromosome Location	chr19:41883198-41883199
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	EBF1	chr19:41882899-41883248	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:41881952-41883286	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr19:41882991-41883243	U87	brain:	n/a	n/a
4	RUNX3	chr19:41882904-41883354	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:41882182-41883533	A549	lung:	n/a	n/a
6	BCL3	chr19:41881874-41883724	A549	lung:	n/a	chr19:41882570-41882579
7	POLR2A	chr19:41882176-41883384	K562	blood:	n/a	n/a
8	PBX3	chr19:41882144-41883695	A549	lung:	n/a	n/a
9	CREB1	chr19:41882272-41883236	A549	lung:	n/a	n/a
10	POLR2A	chr19:41882293-41883272	HL-60	blood:	n/a	n/a
11	MTA3	chr19:41882030-41883338	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:41881878-41883460	HepG2	liver:	n/a	n/a
13	TCF12	chr19:41881959-41883493	A549	lung:	n/a	n/a
14	POLR2A	chr19:41882678-41883213	K562	blood:	n/a	n/a
15	RUNX3	chr19:41882945-41883383	GM12878	blood:	n/a	n/a
16	STAT5A	chr19:41882921-41883464	GM12878	blood:	n/a	n/a
17	POLR2A	chr19:41882150-41883300	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr19:41882952-41883262	GM12878	blood:	n/a	n/a
19	BCL3	chr19:41881822-41883679	A549	lung:	n/a	chr19:41882570-41882579
20	POLR2A	chr19:41882740-41883262	K562	blood:	n/a	n/a
21	POLR2A	chr19:41882809-41883279	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:41882074..41885616-chr19:41888544..41893640,5	K562	blood:
2	chr19:41869853..41871782-chr19:41881681..41884054,2	K562	blood:

Variant related genes	Relation type
BCKDHA	TF binding region
TMEM91	TF binding region
ENSG00000123810	Chromatin interaction
ENSG00000142046	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12983789	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4802123	1.00[CHB][hapmap]
rs4803464	0.82[ASW][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];1.00[YRI][hapmap]
rs8179181	1.00[CHB][hapmap]
rs887499	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv996035	chr19:41881445-41887549	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1529717	CCDC114	cis	parietal	SCAN
rs1529717	ZFP112	cis	parietal	SCAN
rs1529717	PSG2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41871200-41884000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr19:41871200-41888600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41871400-41888400	Weak transcription	Dnd41	blood
4	chr19:41880400-41894000	Weak transcription	HSMMtube	muscle
5	chr19:41881800-41883200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr19:41881800-41883400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr19:41882000-41883200	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:41882000-41883200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr19:41882000-41883200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:41882000-41883200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:41882000-41883200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr19:41882000-41883200	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr19:41882000-41883200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:41882000-41883200	Flanking Active TSS	Primary B cells from cord blood	blood
15	chr19:41882000-41883200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr19:41882000-41883200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:41882000-41883200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr19:41882000-41883200	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr19:41882000-41883200	Active TSS	Brain Cingulate Gyrus	brain
20	chr19:41882000-41883200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr19:41882000-41883200	Flanking Active TSS	Fetal Stomach	stomach
22	chr19:41882000-41883200	Flanking Active TSS	Rectal Smooth Muscle	rectum
23	chr19:41882000-41883200	Flanking Active TSS	HMEC	breast
24	chr19:41882000-41883200	Flanking Active TSS	NHEK	skin
25	chr19:41882000-41883200	Flanking Active TSS	Osteobl	bone
26	chr19:41882000-41883400	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr19:41882000-41883400	Flanking Active TSS	Brain Germinal Matrix	brain
28	chr19:41882000-41883600	Enhancers	Spleen	Spleen
29	chr19:41882200-41883200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr19:41882200-41883200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr19:41882200-41883200	Active TSS	Brain Angular Gyrus	brain
32	chr19:41882200-41883200	Flanking Active TSS	Ovary	ovary
33	chr19:41882200-41883400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr19:41882200-41883400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr19:41882200-41883400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr19:41882400-41883200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:41882400-41883200	Active TSS	Duodenum Mucosa	Duodenum
38	chr19:41882400-41883200	Enhancers	Fetal Heart	heart
39	chr19:41882400-41883200	Active TSS	Rectal Mucosa Donor 29	rectum
40	chr19:41882600-41883200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:41882600-41883200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:41882600-41883200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr19:41882600-41883200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:41882600-41883200	Active TSS	Brain Hippocampus Middle	brain
45	chr19:41882600-41883200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:41882600-41884400	Enhancers	GM12878-XiMat	blood
47	chr19:41882800-41883200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
48	chr19:41882800-41883200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:41882800-41883200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
50	chr19:41882800-41883200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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