Variant report

Variant	rs2350962
Chromosome Location	chr17:17614097-17614098
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17612962..17614544-chr17:17715289..17718001,2	MCF-7	breast:
2	chr17:17612154..17614264-chr17:17622183..17624115,2	K562	blood:
3	chr17:17612942..17614655-chr17:17676717..17679222,2	MCF-7	breast:
4	chr17:17612996..17615651-chr17:17616150..17617784,2	K562	blood:
5	chr17:17606494..17609263-chr17:17609958..17614352,4	K562	blood:
6	chr17:17604773..17606317-chr17:17612644..17614425,2	K562	blood:

Variant related genes	Relation type
ENSG00000207839	Chromatin interaction
ENSG00000072310	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12938840	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12938914	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2001421	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2882552	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs4074643	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4244601	0.87[JPT][hapmap]
rs4636969	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924813	0.86[JPT][hapmap]
rs4925103	0.93[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs4995264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720856	0.81[JPT][hapmap]
rs7209595	0.88[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7213879	0.93[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7225141	0.88[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs8067800	0.89[EUR][1000 genomes]
rs8071107	0.84[CEU][hapmap];0.90[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap]
rs9899364	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs9900148	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9905702	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9907986	0.93[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
6	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
7	nsv907753	chr17:17573539-17747289	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv907754	chr17:17573539-17782404	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
9	nsv1061126	chr17:17578826-17803194	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv543238	chr17:17578826-17803194	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
11	nsv833385	chr17:17594037-17765578	Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
12	nsv1058884	chr17:17594370-17803194	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
13	nsv543240	chr17:17594370-17803194	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv543241	chr17:17596222-17703059	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1064176	chr17:17596222-17803194	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
16	nsv543242	chr17:17596222-17803194	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1062361	chr17:17598407-17746899	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
18	nsv543243	chr17:17598407-17746899	Genic enhancers Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2350962	LLGL1	cis	parietal	SCAN
rs2350962	TOM1L2	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17599200-17615600	Weak transcription	Primary B cells from cord blood	blood
2	chr17:17599400-17617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr17:17599400-17617400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:17600400-17614800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr17:17601400-17617600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:17604800-17614600	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr17:17604800-17614600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr17:17605600-17614400	Weak transcription	Brain Substantia Nigra	brain
9	chr17:17606400-17614600	Weak transcription	Fetal Kidney	kidney
10	chr17:17606400-17615600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:17607200-17614200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr17:17607400-17614600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr17:17608000-17614400	Weak transcription	Brain Germinal Matrix	brain
14	chr17:17608600-17614600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr17:17608600-17620400	Weak transcription	Dnd41	blood
16	chr17:17608800-17615600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:17609200-17616600	Enhancers	Fetal Intestine Large	intestine
18	chr17:17609400-17614200	Genic enhancers	Fetal Intestine Small	intestine
19	chr17:17609400-17614400	Enhancers	HepG2	liver
20	chr17:17609400-17618200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:17610000-17615600	Weak transcription	Liver	Liver
22	chr17:17610400-17614200	Weak transcription	Fetal Brain Female	brain
23	chr17:17611000-17614400	Weak transcription	GM12878-XiMat	blood
24	chr17:17611000-17616000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr17:17611400-17616000	Enhancers	Fetal Lung	lung
26	chr17:17611400-17617600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:17612200-17616200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:17612200-17617000	Weak transcription	Adipose Nuclei	Adipose
29	chr17:17612400-17615800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr17:17612600-17614400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
31	chr17:17612600-17616000	Enhancers	Lung	lung
32	chr17:17612600-17616200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:17612600-17616200	Enhancers	Placenta Amnion	Placenta Amnion
34	chr17:17612600-17616400	Enhancers	Stomach Mucosa	stomach
35	chr17:17612800-17614800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:17612800-17615400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:17612800-17616000	Enhancers	Pancreas	Pancrea
38	chr17:17612800-17618000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr17:17613000-17614200	Weak transcription	Fetal Thymus	thymus
40	chr17:17613000-17618400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:17613200-17614200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr17:17613200-17614400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:17613200-17614600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr17:17613200-17615000	Enhancers	Colonic Mucosa	Colon
45	chr17:17613200-17615400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:17613200-17616000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr17:17613200-17616000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:17613200-17616000	Enhancers	Right Ventricle	heart
49	chr17:17613200-17616200	Enhancers	Brain Anterior Caudate	brain
50	chr17:17613200-17616200	Enhancers	Left Ventricle	heart

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