Variant report

Variant	rs16941569
Chromosome Location	chr17:45163078-45163079
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45159211..45163683-chr17:45163741..45168313,5	K562	blood:
2	chr17:45145658..45148463-chr17:45161187..45163786,2	MCF-7	breast:
3	chr17:45162074..45163604-chr17:45171046..45173992,2	MCF-7	breast:
4	chr17:45156502..45159050-chr17:45162212..45165184,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11079751	0.91[ASN][1000 genomes]
rs11570492	1.00[YRI][hapmap]
rs11570579	0.84[GIH][hapmap]
rs11570584	0.87[YRI][hapmap]
rs11649831	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11650241	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11654437	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11657664	0.84[AFR][1000 genomes]
rs11869037	0.87[LWK][hapmap]
rs12452715	0.91[ASN][1000 genomes]
rs16941626	0.81[GIH][hapmap]
rs16941635	0.81[GIH][hapmap]
rs2678713	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28376067	0.82[ASN][1000 genomes]
rs2907245	0.80[ASN][1000 genomes]
rs2959964	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs35936425	0.95[ASN][1000 genomes]
rs56023235	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56200895	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57418075	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6504778	0.87[YRI][hapmap]
rs7217466	0.87[YRI][hapmap]
rs73308962	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8067246	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs8078960	0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3502492	chr17:44305975-45169159	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	esv3502493	chr17:44305975-45169159	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv522797	chr17:45084279-45183152	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	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
8	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
9	esv21010	chr17:45125753-45177221	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv521632	chr17:45151549-45196190	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16941569	KRT31	cis	parietal	SCAN
rs16941569	MYL4	cis	lung	GTEx
rs16941569	IGFBP4	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45145000-45163600	Weak transcription	Aorta	Aorta
2	chr17:45145000-45163800	Weak transcription	Small Intestine	intestine
3	chr17:45145000-45164600	Weak transcription	Brain Angular Gyrus	brain
4	chr17:45145000-45169800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr17:45145000-45169800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr17:45145000-45169800	Weak transcription	Fetal Lung	lung
7	chr17:45145000-45176400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:45145000-45176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr17:45145000-45176800	Weak transcription	Lung	lung
10	chr17:45145200-45169200	Weak transcription	Primary B cells from cord blood	blood
11	chr17:45145200-45170200	Weak transcription	Brain Germinal Matrix	brain
12	chr17:45145200-45176600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr17:45145400-45176000	Weak transcription	Primary T cells from cord blood	blood
14	chr17:45146400-45169800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr17:45146400-45170800	Weak transcription	Dnd41	blood
16	chr17:45148800-45175400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr17:45149000-45164200	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr17:45149000-45168600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr17:45149000-45170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:45149000-45173800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr17:45149600-45175400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr17:45149600-45176800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr17:45150200-45170000	Weak transcription	Ovary	ovary
24	chr17:45150200-45174600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:45150600-45164600	Weak transcription	Brain Anterior Caudate	brain
26	chr17:45150600-45167200	Weak transcription	Spleen	Spleen
27	chr17:45150600-45169800	Weak transcription	Fetal Muscle Leg	muscle
28	chr17:45150600-45170600	Weak transcription	HSMM	muscle
29	chr17:45150600-45176400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:45150600-45176800	Weak transcription	Left Ventricle	heart
31	chr17:45155000-45169800	Weak transcription	Fetal Brain Female	brain
32	chr17:45155600-45170200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr17:45155600-45170200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:45155600-45170200	Weak transcription	NHEK	skin
35	chr17:45155600-45173600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr17:45158200-45170600	Weak transcription	A549	lung
37	chr17:45158600-45169800	Weak transcription	Fetal Thymus	thymus
38	chr17:45158600-45175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr17:45159200-45175600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr17:45159600-45169800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr17:45159800-45169800	Weak transcription	Fetal Stomach	stomach
42	chr17:45159800-45170200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr17:45161200-45164400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr17:45161800-45163200	Enhancers	Fetal Intestine Large	intestine
45	chr17:45162200-45163800	Enhancers	HepG2	liver
46	chr17:45162200-45164200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr17:45162400-45163200	Enhancers	Duodenum Mucosa	Duodenum
48	chr17:45162400-45163200	Enhancers	K562	blood
49	chr17:45162400-45163800	Enhancers	Fetal Intestine Small	intestine
50	chr17:45162400-45164200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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