Variant report

Variant	rs16941306
Chromosome Location	chr17:45010552-45010553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:45008062..45010873-chr17:45025495..45027532,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10491148	1.00[CEU][hapmap]
rs11871306	1.00[CEU][hapmap]
rs1638450	1.00[CEU][hapmap]
rs16941271	1.00[CEU][hapmap];0.80[AFR][1000 genomes]
rs16941273	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.80[AFR][1000 genomes]
rs16941300	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs16941312	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16941317	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16941318	0.82[ASW][hapmap];1.00[CEU][hapmap]
rs16941324	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs16941373	0.87[EUR][1000 genomes]
rs16941378	0.87[EUR][1000 genomes]
rs16941390	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs197935	1.00[CEU][hapmap]
rs2003540	0.87[EUR][1000 genomes]
rs754474	1.00[CEU][hapmap]
rs8082211	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3492820	chr17:44174959-45161556	Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv3492821	chr17:44174959-45161556	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv531823	chr17:44485771-45067769	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv908562	chr17:44828931-45102413	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv949295	chr17:44836653-45080757	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases
8	nsv428672	chr17:44872446-45023425	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067211	chr17:44979111-45057620	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
10	nsv543378	chr17:44979111-45057620	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16941306	NUFIP2	trans	brain	seeQTL
rs16941306	SLC5A3	trans	brain	seeQTL
rs16941306	BEND5	trans	brain	seeQTL
rs16941306	KIAA1549	trans	brain	seeQTL
rs16941306	LAMB3	trans	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45001200-45011400	Weak transcription	Fetal Brain Male	brain
2	chr17:45001600-45020800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:45002000-45021000	Weak transcription	Fetal Heart	heart
4	chr17:45002800-45020000	Strong transcription	Fetal Muscle Leg	muscle
5	chr17:45004200-45018400	Strong transcription	Primary T cells from cord blood	blood
6	chr17:45004800-45018200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr17:45005000-45019800	Strong transcription	GM12878-XiMat	blood
8	chr17:45005200-45018000	Strong transcription	Primary B cells from cord blood	blood
9	chr17:45005200-45018800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr17:45005400-45017800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:45005400-45018400	Strong transcription	Fetal Stomach	stomach
12	chr17:45005400-45018800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr17:45005600-45018600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:45005600-45020200	Strong transcription	Fetal Thymus	thymus
15	chr17:45005800-45019800	Strong transcription	Fetal Muscle Trunk	muscle
16	chr17:45005800-45020000	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr17:45006000-45012000	Strong transcription	K562	blood
18	chr17:45006000-45012800	Strong transcription	Hela-S3	cervix
19	chr17:45006000-45018400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr17:45006200-45018400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr17:45006200-45018400	Strong transcription	Thymus	Thymus
22	chr17:45006200-45020000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr17:45006400-45014400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr17:45006400-45018000	Strong transcription	Ovary	ovary
25	chr17:45006400-45018400	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr17:45006400-45018400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr17:45006400-45018600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr17:45006600-45014200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
29	chr17:45006600-45014800	Strong transcription	Primary hematopoietic stem cells	blood
30	chr17:45006600-45018200	Strong transcription	Adipose Nuclei	Adipose
31	chr17:45006600-45019000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr17:45006600-45019800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr17:45006800-45013200	Strong transcription	Gastric	stomach
34	chr17:45006800-45013400	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr17:45006800-45014200	Strong transcription	Psoas Muscle	Psoas
36	chr17:45006800-45015200	Strong transcription	Right Ventricle	heart
37	chr17:45006800-45017800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr17:45006800-45018000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr17:45006800-45018000	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr17:45006800-45018000	Strong transcription	HepG2	liver
41	chr17:45006800-45018200	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr17:45006800-45018200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:45006800-45018200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr17:45006800-45018200	Strong transcription	Fetal Brain Female	brain
45	chr17:45006800-45018200	Strong transcription	Placenta	Placenta
46	chr17:45006800-45018200	Strong transcription	Pancreas	Pancrea
47	chr17:45006800-45018200	Strong transcription	Rectal Smooth Muscle	rectum
48	chr17:45006800-45018200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr17:45006800-45018600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr17:45006800-45018800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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