Variant report

Variant	rs17707021
Chromosome Location	chr19:37018202-37018203
allele	G/T
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:13)
LncRNA
region (count:0)
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	CHD1	chr19:37018052-37020289	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:37017926-37020021	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36978821..36980790-chr19:37017858..37020685,3	K562	blood:
2	chr19:37016297..37018434-chr19:37262581..37265198,2	K562	blood:
3	chr19:37017743..37019603-chr19:37263003..37264867,2	MCF-7	breast:
4	chr19:37014827..37016384-chr19:37017913..37020178,2	K562	blood:
5	chr19:36869703..36871321-chr19:37018127..37020542,2	K562	blood:
6	chr19:37018139..37019685-chr19:37156038..37157932,2	MCF-7	breast:
7	chr19:36979124..36982554-chr19:37017679..37020247,4	MCF-7	breast:
8	chr19:36978148..36981795-chr19:37018105..37021194,8	K562	blood:
9	chr19:37017852..37021325-chr19:37033943..37038779,6	K562	blood:
10	chr19:36628146..36630638-chr19:37017222..37019646,2	K562	blood:
11	chr19:37012845..37016384-chr19:37017166..37020287,4	K562	blood:
12	chr19:37017989..37021035-chr19:37064029..37066517,3	MCF-7	breast:
13	chr19:37017864..37019585-chr19:37067468..37069306,2	K562	blood:

No data

Variant related genes	Relation type
ZNF260	TF binding region
ENSG00000228629	TF binding region
ENSG00000142065	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000267041	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000267260	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000197808	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000267309	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs17707014	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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4514798	0.84[AFR][1000 genomes];0.85[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];0.87[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes]
rs4806333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4806340	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs55634974	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55743839	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55801623	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55830504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55880628	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55933007	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56054915	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56075402	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56183102	0.87[AMR][1000 genomes]
rs56246998	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs57126710	0.87[ASN][1000 genomes]
rs6510549	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7249099	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7257899	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7259057	0.87[AMR][1000 genomes]
rs73032465	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73032484	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032491	0.87[ASN][1000 genomes]
rs73032502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034106	0.87[ASN][1000 genomes]
rs73034109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034142	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034176	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73036297	0.81[AMR][1000 genomes]
rs73038105	0.81[AMR][1000 genomes]
rs73049817	0.90[AMR][1000 genomes]
rs73049826	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73049844	0.81[AMR][1000 genomes]
rs73049851	0.85[AMR][1000 genomes]
rs73049853	0.85[AMR][1000 genomes]
rs8100340	0.89[AFR][1000 genomes];1.00[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	0.85[AMR][1000 genomes]
rs8104893	0.90[AMR][1000 genomes]
rs8106144	0.87[ASN][1000 genomes]
rs8108848	1.00[JPT][hapmap]
rs8110140	0.87[AMR][1000 genomes]
rs8111192	0.87[AFR][1000 genomes];0.90[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17707021	IL29	cis	parietal	SCAN
rs17707021	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs17707021	HNRNPUL1	cis	parietal	SCAN
rs17707021	CLC	cis	cerebellum	SCAN
rs17707021	CADM4	cis	cerebellum	SCAN
rs17707021	PLD3	cis	cerebellum	SCAN
rs17707021	PVR	cis	cerebellum	SCAN
rs17707021	ZNF285	cis	parietal	SCAN
rs17707021	PLD3	cis	parietal	SCAN
rs17707021	CIC	cis	cerebellum	SCAN
rs17707021	PRR19	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37003800-37018600	ZNF genes & repeats	A549	lung
2	chr19:37009000-37018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:37009400-37018400	Weak transcription	Stomach Mucosa	stomach
4	chr19:37012000-37018400	Weak transcription	Gastric	stomach
5	chr19:37013400-37018400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr19:37016200-37018400	Weak transcription	Placenta	Placenta
7	chr19:37016200-37018400	Weak transcription	Psoas Muscle	Psoas
8	chr19:37016400-37018400	Weak transcription	Left Ventricle	heart
9	chr19:37016600-37018400	Weak transcription	Aorta	Aorta
10	chr19:37016600-37018400	Weak transcription	Fetal Thymus	thymus
11	chr19:37016600-37018400	Weak transcription	Ovary	ovary
12	chr19:37017000-37018400	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr19:37017000-37018400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:37017200-37018400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr19:37017600-37018400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:37017600-37018400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr19:37017600-37018400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:37017600-37018400	Enhancers	Brain Cingulate Gyrus	brain
19	chr19:37017600-37018400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr19:37017600-37018400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr19:37017600-37018400	Enhancers	Thymus	Thymus
22	chr19:37017600-37018600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:37017600-37018600	Transcr. at gene 5' and 3'	Fetal Brain Male	brain
24	chr19:37017600-37018800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:37017600-37019000	Active TSS	Right Atrium	heart
26	chr19:37017600-37020600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr19:37017600-37020600	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr19:37017800-37018400	Enhancers	Primary B cells from peripheral blood	blood
29	chr19:37017800-37018400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr19:37017800-37018400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr19:37017800-37018400	Enhancers	Brain Anterior Caudate	brain
32	chr19:37017800-37018400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:37017800-37018400	Weak transcription	Fetal Intestine Large	intestine
34	chr19:37017800-37018400	Enhancers	Placenta Amnion	Placenta Amnion
35	chr19:37017800-37018600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:37017800-37018600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr19:37017800-37018600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr19:37017800-37018600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr19:37017800-37018600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr19:37017800-37018600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr19:37017800-37018600	Flanking Active TSS	Osteobl	bone
42	chr19:37017800-37018800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr19:37017800-37018800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr19:37017800-37018800	Flanking Active TSS	Liver	Liver
45	chr19:37017800-37018800	Enhancers	Pancreas	Pancrea
46	chr19:37017800-37019000	Flanking Active TSS	Primary hematopoietic stem cells	blood
47	chr19:37017800-37019600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:37017800-37019800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:37017800-37019800	Active TSS	Fetal Kidney	kidney
50	chr19:37017800-37020000	Active TSS	Right Ventricle	heart

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