Variant report

Variant	rs16941626
Chromosome Location	chr17:45255340-45255341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:45249463..45251128-chr17:45254076..45256037,2	K562	blood:
2	chr17:45252680..45255681-chr17:45273167..45275450,3	K562	blood:
3	chr17:45252679..45255375-chr17:45295130..45298043,2	K562	blood:
4	chr17:45253169..45255870-chr17:45262068..45264746,2	MCF-7	breast:
5	chr17:45246078..45249140-chr17:45252023..45255438,3	K562	blood:

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

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11079757	0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs11570481	0.89[ASN][1000 genomes]
rs11570495	0.89[ASN][1000 genomes]
rs11570513	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11570548	0.86[ASN][1000 genomes]
rs11570565	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11570579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16941628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941635	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1986817	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55706273	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55887846	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56287938	0.86[ASN][1000 genomes]
rs59349147	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs717162	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16941626	PSMC3IP	cis	cerebellum	SCAN
rs16941626	MYL4	cis	lung	GTEx
rs16941626	KRTAP4-1	cis	parietal	SCAN
rs16941626	IGFBP4	cis	parietal	SCAN
rs16941626	MYL4	cis	Esophagus Muscularis	GTEx
rs16941626	MYL4	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45247600-45255400	Strong transcription	HepG2	liver
2	chr17:45249400-45256200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:45249600-45255400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr17:45249600-45255600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr17:45249600-45255600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr17:45249600-45256200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:45249600-45256200	Weak transcription	NHLF	lung
8	chr17:45249600-45256400	Weak transcription	Brain Angular Gyrus	brain
9	chr17:45249600-45256400	Weak transcription	Fetal Kidney	kidney
10	chr17:45249600-45256400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr17:45249600-45256400	Weak transcription	Spleen	Spleen
12	chr17:45249600-45256400	Weak transcription	HSMMtube	muscle
13	chr17:45249600-45256600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr17:45249600-45256600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr17:45249600-45256600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr17:45249600-45257400	Weak transcription	Lung	lung
17	chr17:45249600-45258400	Weak transcription	Left Ventricle	heart
18	chr17:45249600-45258400	Strong transcription	Dnd41	blood
19	chr17:45249600-45258800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr17:45249600-45258800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr17:45249600-45258800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:45249600-45258800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr17:45249600-45258800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr17:45249600-45258800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:45249600-45258800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:45249600-45258800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:45249600-45258800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr17:45249600-45258800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr17:45249600-45258800	Weak transcription	Aorta	Aorta
30	chr17:45249600-45258800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr17:45249600-45258800	Weak transcription	Brain Hippocampus Middle	brain
32	chr17:45249600-45258800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr17:45249600-45258800	Weak transcription	Brain Substantia Nigra	brain
34	chr17:45249600-45258800	Weak transcription	Colonic Mucosa	Colon
35	chr17:45249600-45258800	Weak transcription	Esophagus	oesophagus
36	chr17:45249600-45258800	Weak transcription	Fetal Brain Male	brain
37	chr17:45249600-45258800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr17:45249600-45258800	Weak transcription	Gastric	stomach
39	chr17:45249600-45258800	Weak transcription	Pancreas	Pancrea
40	chr17:45249600-45258800	Weak transcription	Psoas Muscle	Psoas
41	chr17:45249600-45258800	Weak transcription	Right Atrium	heart
42	chr17:45249600-45258800	Weak transcription	Small Intestine	intestine
43	chr17:45249600-45258800	Weak transcription	Stomach Mucosa	stomach
44	chr17:45249800-45258800	Strong transcription	Fetal Thymus	thymus
45	chr17:45250000-45258800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:45250200-45258200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr17:45250200-45258400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr17:45250200-45258800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr17:45250400-45258400	Strong transcription	A549	lung
50	chr17:45250400-45258800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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