Variant report

Variant	rs16941622
Chromosome Location	chr17:45252889-45252890
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45252852..45255226-chr17:45287274..45289191,2	K562	blood:
2	chr17:45252680..45255681-chr17:45273167..45275450,3	K562	blood:
3	chr17:45252679..45255375-chr17:45295130..45298043,2	K562	blood:
4	chr17:45246078..45249140-chr17:45252023..45255438,3	K562	blood:
5	chr17:45250177..45252891-chr17:45399741..45402575,2	K562	blood:

Variant related genes	Relation type
ENSG00000178852	Chromatin interaction
ENSG00000004897	Chromatin interaction
ENSG00000263293	Chromatin interaction
ENSG00000252088	Chromatin interaction
ENSG00000261872	Chromatin interaction
ENSG00000198336	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11079760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11570468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11570511	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11570546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12601027	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs16941662	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3785874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3809858	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58422248	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs66945411	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67305320	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67861319	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72823428	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	esv3584	chr17:45246216-45265642	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3790	chr17:45247093-45261518	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv3344584	chr17:45247298-45258989	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv6873	chr17:45247370-45266575	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv3438623	chr17:45249255-45266618	Genic enhancers Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3437669	chr17:45249306-45259022	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv8330	chr17:45249307-45266621	Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv3314728	chr17:45249324-45258982	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3314730	chr17:45249324-45258982	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv3431737	chr17:45249325-45259054	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	esv3374428	chr17:45249343-45266580	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	esv3362151	chr17:45249372-45258977	ZNF genes & repeats Strong transcription Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv3450592	chr17:45249392-45258947	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16941622	RPS4Y1	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45246800-45254400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr17:45247600-45255400	Strong transcription	HepG2	liver
3	chr17:45249400-45256200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr17:45249600-45253000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr17:45249600-45253200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:45249600-45253400	Strong transcription	Primary B cells from cord blood	blood
7	chr17:45249600-45253600	Weak transcription	Colon Smooth Muscle	Colon
8	chr17:45249600-45253800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:45249600-45253800	Weak transcription	Hela-S3	cervix
10	chr17:45249600-45254000	Weak transcription	Fetal Lung	lung
11	chr17:45249600-45254000	Weak transcription	HMEC	breast
12	chr17:45249600-45254400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:45249600-45254400	Weak transcription	Placenta	Placenta
14	chr17:45249600-45254600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:45249600-45254600	Weak transcription	Brain Anterior Caudate	brain
16	chr17:45249600-45254800	Weak transcription	Ovary	ovary
17	chr17:45249600-45255200	Weak transcription	Fetal Heart	heart
18	chr17:45249600-45255200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr17:45249600-45255400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr17:45249600-45255600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr17:45249600-45255600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr17:45249600-45256200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:45249600-45256200	Weak transcription	NHLF	lung
24	chr17:45249600-45256400	Weak transcription	Brain Angular Gyrus	brain
25	chr17:45249600-45256400	Weak transcription	Fetal Kidney	kidney
26	chr17:45249600-45256400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr17:45249600-45256400	Weak transcription	Spleen	Spleen
28	chr17:45249600-45256400	Weak transcription	HSMMtube	muscle
29	chr17:45249600-45256600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:45249600-45256600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr17:45249600-45256600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr17:45249600-45257400	Weak transcription	Lung	lung
33	chr17:45249600-45258400	Weak transcription	Left Ventricle	heart
34	chr17:45249600-45258400	Strong transcription	Dnd41	blood
35	chr17:45249600-45258800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr17:45249600-45258800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr17:45249600-45258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr17:45249600-45258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr17:45249600-45258800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr17:45249600-45258800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:45249600-45258800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr17:45249600-45258800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:45249600-45258800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr17:45249600-45258800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr17:45249600-45258800	Weak transcription	Aorta	Aorta
46	chr17:45249600-45258800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr17:45249600-45258800	Weak transcription	Brain Hippocampus Middle	brain
48	chr17:45249600-45258800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr17:45249600-45258800	Weak transcription	Brain Substantia Nigra	brain
50	chr17:45249600-45258800	Weak transcription	Colonic Mucosa	Colon

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