Variant report

Variant	rs692257
Chromosome Location	chr19:39645350-39645351
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	CTCF	chr19:39645241-39645404	MCF-7	breast:	n/a	n/a
2	MAZ	chr19:39645287-39645593	K562	blood:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
3	CTCF	chr19:39645234-39645374	MCF-7	breast:	n/a	n/a
4	MAX	chr19:39644984-39645802	ECC-1	luminal epithelium:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
5	CTCF	chr19:39645234-39645363	K562	blood:	n/a	n/a
6	MAX	chr19:39645157-39645634	H1-hESC	embryonic stem cell:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
7	USF1	chr19:39645309-39645516	SK-N-SH_RA	brain:	n/a	chr19:39645398-39645409
8	CTCF	chr19:39645260-39645410	HepG2	liver:	n/a	n/a
9	SIN3AK20	chr19:39644790-39646296	MCF-7	breast:	n/a	n/a
10	CTCF	chr19:39645240-39645390	SK-N-SH_RA	brain:	n/a	n/a
11	GABPA	chr19:39645045-39645852	MCF-7	breast:	n/a	n/a
12	CTCF	chr19:39645229-39645383	NHEK	skin:	n/a	n/a
13	NFIC	chr19:39645083-39645692	ECC-1	luminal epithelium:	n/a	n/a
14	HA-E2F1	chr19:39644953-39645808	MCF-7	breast:	n/a	chr19:39645163-39645174
15	MYC	chr19:39645330-39645433	MCF-7	breast:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
16	CTCF	chr19:39645239-39645381	H1-hESC	embryonic stem cell:	n/a	n/a
17	ZBTB7A	chr19:39645244-39645469	K562	blood:	n/a	n/a
18	ELF1	chr19:39645200-39645649	K562	blood:	n/a	n/a
19	FOXA1	chr19:39645208-39645736	T-47D	breast:	n/a	n/a
20	GATA3	chr19:39645188-39645893	T-47D	breast:	n/a	chr19:39645214-39645224
21	CTCF	chr19:39645220-39645409	K562	blood:	n/a	n/a
22	POLR2A	chr19:39645328-39645358	MCF-7	breast:	n/a	n/a
23	MYC	chr19:39645314-39645498	K562	blood:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
24	GATA3	chr19:39645161-39645857	T-47D	breast:	n/a	chr19:39645214-39645224
25	NR2F2	chr19:39645072-39646001	MCF-7	breast:	n/a	n/a
26	USF1	chr19:39645096-39645781	HCT-116	colon:	n/a	chr19:39645398-39645409
27	MAX	chr19:39645191-39645624	H1-hESC	embryonic stem cell:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
28	MAX	chr19:39644653-39646265	MCF-7	breast:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
29	RAD21	chr19:39645226-39645451	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr19:39645200-39645350	BE2_C	brain:	n/a	n/a
31	MAX	chr19:39644913-39645814	HCT-116	colon:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
32	GATA3	chr19:39644826-39646058	MCF-7	breast:	n/a	chr19:39645214-39645224 chr19:39645069-39645079
33	CTCF	chr19:39645200-39645350	HEEpiC	esophagus:	n/a	n/a
34	MAX	chr19:39645248-39645562	K562	blood:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
35	CTCF	chr19:39645200-39645350	MCF-7	breast:	n/a	n/a
36	USF2	chr19:39645282-39645471	K562	blood:	n/a	n/a
37	CTCF	chr19:39645200-39645350	SK-N-SH_RA	brain:	n/a	n/a
38	SIN3A	chr19:39645256-39645563	H1-hESC	embryonic stem cell:	n/a	chr19:39645526-39645539 chr19:39645400-39645409
39	MAX	chr19:39645268-39645479	K562	blood:	n/a	chr19:39645399-39645409 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645399-39645408 chr19:39645397-39645406
40	TCF12	chr19:39645063-39645667	ECC-1	luminal epithelium:	n/a	n/a
41	USF2	chr19:39645235-39645590	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr19:39645113-39645554	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr19:39645280-39645430	NHEK	skin:	n/a	n/a
44	POLR2A	chr19:39645269-39645837	MCF-7	breast:	n/a	n/a
45	CTCF	chr19:39645273-39645353	Pancreas_OC	pancreas:	n/a	n/a
46	USF1	chr19:39645117-39645697	ECC-1	luminal epithelium:	n/a	chr19:39645398-39645409
47	CTCF	chr19:39645265-39645352	MCF-7	breast:	n/a	n/a
48	USF1	chr19:39645106-39645605	H1-hESC	embryonic stem cell:	n/a	chr19:39645398-39645409
49	USF1	chr19:39645179-39645613	H1-hESC	embryonic stem cell:	n/a	chr19:39645398-39645409
50	USF1	chr19:39645206-39645619	K562	blood:	n/a	chr19:39645398-39645409

No.	Distal block	Cell Line	Cell type
1	chr19:39643758..39646287-chr19:39649616..39652008,3	K562	blood:
2	chr19:39612929..39614547-chr19:39644614..39646235,2	K562	blood:
3	chr19:39613047..39614883-chr19:39644735..39646568,2	K562	blood:
4	chr19:39643019..39646132-chr19:39671022..39674035,4	MCF-7	breast:
5	chr19:39522254..39524021-chr19:39644088..39646362,2	MCF-7	breast:
6	chr19:39644386..39647038-chr19:39665325..39668037,2	MCF-7	breast:
7	chr19:39645159..39645930-chr19:39677797..39678451,2	K562	blood:
8	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
9	chr19:39643809..39645925-chr19:39673965..39675850,2	K562	blood:
10	chr19:39643041..39646015-chr19:39653933..39655727,2	K562	blood:
11	chr19:39620592..39621547-chr19:39645122..39646030,2	MCF-7	breast:

Variant related genes	Relation type
PAK4	TF binding region
ENSG00000161243	Chromatin interaction
ENSG00000269172	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12976130	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs12976664	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12977799	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1549927	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs476713	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803208	0.81[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs490249	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs513053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs529336	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550664	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554114	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs576527	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs691080	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs691577	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs692191	0.81[CEU][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs692337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs692468	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs692475	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs692257	PAK4	cis	Thyroid	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:39624000-39647000	Weak transcription	NHLF	lung
5	chr19:39627200-39646800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:39627600-39645800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr19:39630800-39646800	Weak transcription	Osteobl	bone
8	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
9	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:39635400-39645600	Weak transcription	Spleen	Spleen
11	chr19:39635400-39647000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:39635600-39647000	Weak transcription	NH-A	brain
13	chr19:39635600-39647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr19:39635800-39646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr19:39636000-39647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
17	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
18	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
19	chr19:39637000-39645400	Weak transcription	Right Ventricle	heart
20	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
21	chr19:39637200-39647000	Weak transcription	Small Intestine	intestine
22	chr19:39637400-39645800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr19:39637400-39647400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr19:39638000-39645400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:39638000-39646000	Weak transcription	Colon Smooth Muscle	Colon
27	chr19:39638000-39646800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr19:39638200-39648600	Weak transcription	Brain Angular Gyrus	brain
30	chr19:39640000-39646600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:39640000-39647600	Weak transcription	HSMMtube	muscle
32	chr19:39640000-39648400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
34	chr19:39640200-39646600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr19:39640200-39647400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr19:39640200-39647400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:39641000-39646200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:39641200-39649200	Weak transcription	Fetal Brain Female	brain
40	chr19:39641400-39646600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:39641800-39645400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:39641800-39646400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr19:39642000-39649600	Enhancers	Placenta	Placenta
44	chr19:39642200-39646400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:39642200-39647400	Weak transcription	Right Atrium	heart
46	chr19:39642400-39645400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr19:39642400-39645400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:39642400-39645400	Weak transcription	Ovary	ovary
49	chr19:39642400-39646600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr19:39642400-39647000	Weak transcription	HSMM	muscle

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