Variant report

Variant	rs7654
Chromosome Location	chr1:154129630-154129631
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:154129541-154129736	T-47D	breast:	n/a	n/a
2	POLR2A	chr1:154128813-154131557	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:154129407-154130605	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:154128764-154130610	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:154129440-154131641	GM12892	blood:	n/a	n/a
6	JUN	chr1:154129565-154132628	K562	blood:	n/a	chr1:154130854-154130866
7	POLR2A	chr1:154129400-154131372	GM12892	blood:	n/a	n/a
8	POLR2A	chr1:154128827-154130682	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:154129487-154130702	PFSK-1	brain:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153962389..153965646-chr1:154127758..154130394,3	K562	blood:
2	chr1:154128396..154132314-chr1:154154377..154157554,5	MCF-7	breast:
3	chr1:154118375..154121361-chr1:154129138..154131171,2	MCF-7	breast:
4	chr1:154128999..154131626-chr1:154132372..154134998,2	K562	blood:
5	chr1:154121564..154123790-chr1:154128887..154131552,2	K562	blood:
6	chr1:154122896..154125457-chr1:154127729..154131254,3	MCF-7	breast:
7	chr1:153962061..153965297-chr1:154128875..154131798,4	MCF-7	breast:
8	chr1:154128722..154131890-chr1:154192091..154194653,3	K562	blood:

No data

Variant related genes	Relation type
NUP210L	TF binding region
ENSG00000143612	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11265201	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265303	1.00[ASW][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11265310	1.00[ASW][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11265398	0.81[EUR][1000 genomes]
rs12063890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070842	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091348	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs2066134	0.88[GIH][hapmap]
rs4845591	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs4845607	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59550472	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61109915	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6661996	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672584	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9628669	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv946404	chr1:154128123-154130312	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7654	NUP210L	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154124400-154129800	Weak transcription	Left Ventricle	heart
3	chr1:154125000-154130400	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:154125200-154131000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:154125600-154129800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:154125600-154129800	Weak transcription	Gastric	stomach
7	chr1:154125600-154130000	Weak transcription	Brain Germinal Matrix	brain
8	chr1:154126200-154130400	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr1:154126400-154129800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr1:154126400-154129800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:154126400-154130400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:154126400-154133000	Weak transcription	Ovary	ovary
13	chr1:154126400-154146000	Strong transcription	HMEC	breast
14	chr1:154126600-154130200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:154126800-154129800	Strong transcription	GM12878-XiMat	blood
16	chr1:154126800-154130000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr1:154126800-154130200	Weak transcription	Fetal Brain Male	brain
18	chr1:154126800-154131600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr1:154127000-154130200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:154127000-154130200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:154127000-154130200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
22	chr1:154127000-154130200	Strong transcription	Fetal Intestine Small	intestine
23	chr1:154127000-154131800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:154127000-154143400	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr1:154127000-154143600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:154127000-154148400	Strong transcription	Fetal Intestine Large	intestine
27	chr1:154127000-154149600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:154127200-154129800	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:154127200-154130000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:154127200-154131600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:154127200-154131600	Genic enhancers	Placenta	Placenta
32	chr1:154127200-154132400	Genic enhancers	Fetal Thymus	thymus
33	chr1:154127200-154146000	Strong transcription	Fetal Brain Female	brain
34	chr1:154127400-154130000	Weak transcription	Primary B cells from cord blood	blood
35	chr1:154127400-154131200	Strong transcription	Adipose Nuclei	Adipose
36	chr1:154127400-154131400	Weak transcription	Brain Substantia Nigra	brain
37	chr1:154127400-154132800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:154127400-154148200	Strong transcription	Liver	Liver
39	chr1:154127600-154130000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:154127600-154130000	Weak transcription	Spleen	Spleen
41	chr1:154127600-154130200	Weak transcription	Right Atrium	heart
42	chr1:154127600-154130800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:154127600-154131400	Weak transcription	Lung	lung
44	chr1:154127600-154136400	Weak transcription	Right Ventricle	heart
45	chr1:154127600-154136600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:154127600-154136600	Weak transcription	Esophagus	oesophagus
47	chr1:154127600-154148400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr1:154127800-154129800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:154127800-154130200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr1:154127800-154130400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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