Variant report

Variant	rs17707014
Chromosome Location	chr19:37017796-37017797
allele	A/G
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	FOS	chr19:37017525-37018145	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr19:37017532-37018116	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr19:37017532-37018087	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:37016297..37018434-chr19:37262581..37265198,2	K562	blood:
2	chr19:37017743..37019603-chr19:37263003..37264867,2	MCF-7	breast:
3	chr19:36979124..36982554-chr19:37017679..37020247,4	MCF-7	breast:
4	chr19:36628146..36630638-chr19:37017222..37019646,2	K562	blood:
5	chr19:37012845..37016384-chr19:37017166..37020287,4	K562	blood:

Variant related genes	Relation type
ENSG00000228629	TF binding region
ZNF260	TF binding region
ENSG00000186017	Chromatin interaction
ENSG00000267309	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs17707021	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17707033	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2891868	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4514798	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4806328	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes]
rs4806333	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4806340	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes]
rs55634974	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55743839	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55801623	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830504	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55880628	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55933007	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054915	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56075402	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56183102	0.83[AMR][1000 genomes]
rs56246998	0.85[AMR][1000 genomes]
rs57126710	0.87[ASN][1000 genomes]
rs6510549	0.81[AMR][1000 genomes]
rs7249099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7257899	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259057	0.83[AMR][1000 genomes]
rs73032465	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73032484	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032489	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032491	0.87[ASN][1000 genomes]
rs73032502	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034106	0.87[ASN][1000 genomes]
rs73034109	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034142	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034176	0.88[EUR][1000 genomes]
rs73036297	0.85[AMR][1000 genomes]
rs73038105	0.85[AMR][1000 genomes]
rs73049817	0.85[AMR][1000 genomes]
rs73049826	0.85[AMR][1000 genomes]
rs73049844	0.85[AMR][1000 genomes]
rs73049851	0.81[AMR][1000 genomes]
rs73049853	0.81[AMR][1000 genomes]
rs8100340	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8102097	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102474	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8103917	0.81[AMR][1000 genomes]
rs8104893	0.85[AMR][1000 genomes]
rs8106144	0.87[ASN][1000 genomes]
rs8108848	1.00[JPT][hapmap]
rs8110140	0.83[AMR][1000 genomes]
rs8111192	0.85[AMR][1000 genomes];0.87[EUR][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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17707014	PRR19	cis	cerebellum	SCAN
rs17707014	CADM4	cis	cerebellum	SCAN
rs17707014	PLD3	cis	cerebellum	SCAN
rs17707014	PVR	cis	cerebellum	SCAN
rs17707014	CLC	cis	cerebellum	SCAN
rs17707014	ZNF285	cis	parietal	SCAN
rs17707014	PLD3	cis	parietal	SCAN
rs17707014	CIC	cis	cerebellum	SCAN
rs17707014	IL29	cis	parietal	SCAN
rs17707014	HNRNPUL1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36999200-37018000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:37000000-37017800	ZNF genes & repeats	Liver	Liver
3	chr19:37001000-37018000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
4	chr19:37001600-37018200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:37002600-37018000	ZNF genes & repeats	Fetal Brain Female	brain
6	chr19:37003200-37018000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr19:37003800-37018200	ZNF genes & repeats	Brain Germinal Matrix	brain
8	chr19:37003800-37018600	ZNF genes & repeats	A549	lung
9	chr19:37008600-37017800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:37008600-37017800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:37009000-37018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr19:37009200-37017800	Weak transcription	Right Ventricle	heart
13	chr19:37009400-37018400	Weak transcription	Stomach Mucosa	stomach
14	chr19:37011400-37018200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr19:37012000-37018400	Weak transcription	Gastric	stomach
16	chr19:37013400-37018400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:37013600-37018000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
18	chr19:37014200-37017800	Weak transcription	Brain Anterior Caudate	brain
19	chr19:37014200-37017800	Weak transcription	Pancreas	Pancrea
20	chr19:37014400-37017800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr19:37014400-37017800	Weak transcription	Brain Angular Gyrus	brain
22	chr19:37014400-37017800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:37014400-37017800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr19:37014400-37017800	Weak transcription	HSMMtube	muscle
25	chr19:37014400-37017800	Weak transcription	NHLF	lung
26	chr19:37015200-37018000	ZNF genes & repeats	Fetal Intestine Small	intestine
27	chr19:37015400-37018200	ZNF genes & repeats	GM12878-XiMat	blood
28	chr19:37015600-37018000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
29	chr19:37016200-37017800	Weak transcription	HMEC	breast
30	chr19:37016200-37017800	Weak transcription	NHDF-Ad	bronchial
31	chr19:37016200-37018400	Weak transcription	Placenta	Placenta
32	chr19:37016200-37018400	Weak transcription	Psoas Muscle	Psoas
33	chr19:37016400-37017800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr19:37016400-37017800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:37016400-37017800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr19:37016400-37017800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr19:37016400-37017800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:37016400-37017800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr19:37016400-37017800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr19:37016400-37017800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr19:37016400-37017800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr19:37016400-37017800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr19:37016400-37017800	Weak transcription	HUVEC	blood vessel
44	chr19:37016400-37017800	Weak transcription	Osteobl	bone
45	chr19:37016400-37018400	Weak transcription	Left Ventricle	heart
46	chr19:37016600-37017800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr19:37016600-37017800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:37016600-37017800	Weak transcription	Colonic Mucosa	Colon
49	chr19:37016600-37018400	Weak transcription	Aorta	Aorta
50	chr19:37016600-37018400	Weak transcription	Fetal Thymus	thymus

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