Variant report

Variant	rs9916279
Chromosome Location	chr17:38146154-38146155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38145913-38146534	K562	blood:	n/a	n/a
2	POLR2A	chr17:38145530-38146319	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr17:38145904-38146156	K562	blood:	n/a	n/a
4	POLR2A	chr17:38146064-38146257	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr17:38145468-38146476	GM12878	blood:	n/a	n/a
6	POLR2A	chr17:38146134-38146386	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38142439..38144844-chr17:38145990..38148406,3	K562	blood:
2	chr17:38138604..38140537-chr17:38144740..38146417,2	K562	blood:
3	chr17:38143597..38146360-chr17:38172431..38175405,3	K562	blood:
4	chr17:38142013..38147565-chr17:38148653..38154078,9	K562	blood:
5	chr17:38145482..38147201-chr17:38150565..38153241,2	MCF-7	breast:
6	chr17:38139958..38142841-chr17:38144945..38147813,2	MCF-7	breast:
7	chr1:216898478..216901280-chr17:38145496..38147429,2	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD3	TF binding region
ENSG00000108344	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11078932	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555254	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs11555255	0.95[EUR][1000 genomes]
rs11654473	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11655584	1.00[CHD][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2012	0.94[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227316	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs2827	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs36006659	0.98[EUR][1000 genomes]
rs3859188	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58212353	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503529	0.98[EUR][1000 genomes]
rs7217241	0.95[EUR][1000 genomes]
rs7217694	0.96[EUR][1000 genomes]
rs7222093	0.98[EUR][1000 genomes]
rs7222556	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224260	0.94[CEU][hapmap];0.98[EUR][1000 genomes]
rs7225565	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8068076	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8073732	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs8080546	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9894543	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs9912981	0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913535	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]

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	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9916279	CDC6	cis	cerebellum	SCAN
rs9916279	PSMD3	cis	multi-tissue	Pritchard
rs9916279	MED24	cis	Muscle Skeletal	GTEx
rs9916279	KRTAP4-2	cis	parietal	SCAN
rs9916279	SRCIN1	cis	cerebellum	SCAN
rs9916279	GSDMB	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38138600-38149200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:38138600-38154200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr17:38139200-38151400	Strong transcription	NHEK	skin
4	chr17:38139200-38154800	Strong transcription	Fetal Intestine Small	intestine
5	chr17:38139400-38152200	Strong transcription	K562	blood
6	chr17:38139400-38154400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr17:38139400-38155000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:38139600-38151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:38139600-38153600	Strong transcription	HUVEC	blood vessel
10	chr17:38139600-38154400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr17:38139600-38154600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr17:38139600-38154800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:38139600-38155000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr17:38139600-38155200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr17:38139600-38155400	Strong transcription	Placenta	Placenta
16	chr17:38139600-38155600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr17:38139600-38155600	Strong transcription	Fetal Thymus	thymus
18	chr17:38139800-38153800	Strong transcription	Osteobl	bone
19	chr17:38139800-38154400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr17:38139800-38154400	Strong transcription	HMEC	breast
21	chr17:38139800-38154600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr17:38139800-38154600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr17:38139800-38154800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:38139800-38155000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:38139800-38155000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr17:38139800-38155000	Strong transcription	A549	lung
27	chr17:38139800-38155600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr17:38140000-38148800	Strong transcription	Liver	Liver
29	chr17:38140000-38150400	Strong transcription	Fetal Muscle Trunk	muscle
30	chr17:38140000-38150400	Strong transcription	Fetal Muscle Leg	muscle
31	chr17:38140000-38151200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr17:38140000-38152400	Strong transcription	Adipose Nuclei	Adipose
33	chr17:38140000-38153800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:38140000-38153800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
35	chr17:38140000-38154200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr17:38140000-38154200	Strong transcription	Brain Germinal Matrix	brain
37	chr17:38140000-38154200	Strong transcription	Lung	lung
38	chr17:38140000-38154400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr17:38140000-38154400	Strong transcription	Right Ventricle	heart
40	chr17:38140000-38154600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr17:38140000-38154600	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr17:38140000-38154600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr17:38140000-38154600	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr17:38140000-38154600	Strong transcription	Brain Hippocampus Middle	brain
45	chr17:38140000-38154600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr17:38140000-38154600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:38140000-38154600	Strong transcription	Fetal Intestine Large	intestine
48	chr17:38140000-38155000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr17:38140000-38155000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr17:38140000-38155000	Strong transcription	Rectal Smooth Muscle	rectum

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