Variant report

Variant	rs12984418
Chromosome Location	chr19:39642729-39642730
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	POLR2A	chr19:39642420-39643045	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:39641788..39643713-chr19:39934290..39936014,2	MCF-7	breast:
2	chr19:39638971..39643610-chr19:39643688..39647493,10	MCF-7	breast:
3	chr19:39631951..39634842-chr19:39640711..39642927,2	MCF-7	breast:
4	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:

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

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1079442	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11083509	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11083510	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12610624	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12611361	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12611365	0.84[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12611376	0.84[CEU][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17722300	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17795295	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2873913	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34058542	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34110379	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34270590	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34326918	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34808880	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34846983	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35163943	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35591784	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36148214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3889485	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55748546	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61171111	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67248178	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71356838	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71356839	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71356840	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71356841	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs737450	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8107629	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.94[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12984418	GRLF1	cis	cerebellum	SCAN
rs12984418	ZNF155	cis	parietal	SCAN
rs12984418	CEACAM16	cis	cerebellum	SCAN
rs12984418	CXCL17	cis	cerebellum	SCAN

Chromatin state (count:106 , 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	chr19:39631800-39644600	Weak transcription	Primary T cells from cord blood	blood
11	chr19:39635400-39645600	Weak transcription	Spleen	Spleen
12	chr19:39635400-39647000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr19:39635600-39647000	Weak transcription	NH-A	brain
14	chr19:39635600-39647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr19:39635800-39642800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:39635800-39646000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:39636000-39647400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
19	chr19:39636200-39644800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr19:39636400-39645000	Weak transcription	Adipose Nuclei	Adipose
21	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
22	chr19:39636800-39644600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:39636800-39644600	Weak transcription	HMEC	breast
24	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
25	chr19:39637000-39643200	Weak transcription	Esophagus	oesophagus
26	chr19:39637000-39644600	Weak transcription	Colonic Mucosa	Colon
27	chr19:39637000-39644600	Weak transcription	Fetal Kidney	kidney
28	chr19:39637000-39644600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr19:39637000-39645400	Weak transcription	Right Ventricle	heart
30	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
31	chr19:39637200-39644800	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:39637200-39647000	Weak transcription	Small Intestine	intestine
33	chr19:39637400-39644400	Weak transcription	Pancreas	Pancrea
34	chr19:39637400-39644600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:39637400-39644600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr19:39637400-39644600	Weak transcription	Stomach Mucosa	stomach
37	chr19:39637400-39645800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr19:39637400-39647400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr19:39637600-39645200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:39637800-39644600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:39638000-39644600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr19:39638000-39645400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr19:39638000-39646000	Weak transcription	Colon Smooth Muscle	Colon
45	chr19:39638000-39646800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:39638200-39644400	Weak transcription	HepG2	liver
48	chr19:39638200-39644800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:39638200-39644800	Weak transcription	Brain Substantia Nigra	brain
50	chr19:39638200-39648600	Weak transcription	Brain Angular Gyrus	brain

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