Variant report

Variant	rs12601027
Chromosome Location	chr17:45203468-45203469
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11079760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[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];0.88[ASN][1000 genomes]
rs11570468	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11570511	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11570546	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941622	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]
rs3785874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs3809858	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs58422248	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67305320	0.85[AFR][1000 genomes]
rs67861319	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72823428	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12601027	RPS4Y1	trans	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45185600-45206400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr17:45192400-45212800	Weak transcription	Gastric	stomach
3	chr17:45193200-45212800	Weak transcription	Aorta	Aorta
4	chr17:45194000-45209800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr17:45194200-45204600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr17:45194200-45208200	Strong transcription	HUVEC	blood vessel
7	chr17:45194200-45209600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr17:45194200-45209600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr17:45194200-45209800	Strong transcription	Dnd41	blood
10	chr17:45194800-45203600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr17:45194800-45212800	Weak transcription	Colonic Mucosa	Colon
12	chr17:45194800-45214400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr17:45194800-45234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr17:45195400-45209600	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr17:45195400-45209800	Strong transcription	Fetal Thymus	thymus
16	chr17:45195600-45209400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr17:45195800-45212800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:45196000-45205600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr17:45196000-45206400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:45196000-45209600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:45196000-45209800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr17:45196200-45212800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:45196400-45204200	Weak transcription	Lung	lung
24	chr17:45196400-45204200	Weak transcription	Spleen	Spleen
25	chr17:45196400-45212800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:45196400-45212800	Weak transcription	Ovary	ovary
27	chr17:45196600-45207400	Strong transcription	Placenta	Placenta
28	chr17:45196600-45213000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:45196600-45213000	Weak transcription	Esophagus	oesophagus
30	chr17:45197000-45207000	Strong transcription	Fetal Lung	lung
31	chr17:45197200-45206800	Strong transcription	GM12878-XiMat	blood
32	chr17:45197200-45207400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr17:45197200-45209600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr17:45197400-45206400	Strong transcription	Brain Germinal Matrix	brain
35	chr17:45197400-45206800	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr17:45197400-45209800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr17:45197600-45207400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr17:45197600-45209600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr17:45197800-45209400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr17:45197800-45210000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr17:45198000-45206800	Strong transcription	Fetal Muscle Leg	muscle
42	chr17:45198000-45209600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:45198000-45212000	Strong transcription	Fetal Stomach	stomach
44	chr17:45198200-45205000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:45198200-45210200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:45198200-45212800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr17:45198200-45212800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr17:45198200-45212800	Weak transcription	Brain Angular Gyrus	brain
49	chr17:45198400-45203600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr17:45198400-45204200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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