Variant report

Variant	rs10116424
Chromosome Location	chr9:86304965-86304966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:86304892-86305302	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:86303158..86305549-chr9:86307402..86310035,3	K562	blood:
2	chr9:86304049..86306359-chr9:86307807..86310071,2	K562	blood:
3	chr9:86300623..86303382-chr9:86303567..86306899,3	K562	blood:

Variant related genes	Relation type
UBQLN1	TF binding region
ENSG00000135018	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10114717	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10115073	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10121045	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121882	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122131	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10122134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123002	1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124333	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125987	0.86[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10481738	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140184	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140193	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140196	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140213	0.87[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12335711	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340935	0.88[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342901	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12343837	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344615	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345514	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351677	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13284999	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289229	1.00[ASN][1000 genomes]
rs13291631	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13292088	0.88[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294533	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13301956	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780983	1.00[ASN][1000 genomes]
rs2780987	1.00[ASN][1000 genomes]
rs2780988	1.00[ASN][1000 genomes]
rs2780989	1.00[ASN][1000 genomes]
rs2811898	1.00[ASN][1000 genomes]
rs28555298	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3447	1.00[ASN][1000 genomes]
rs34778713	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34891935	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35378833	1.00[ASN][1000 genomes]
rs35535452	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4364707	1.00[ASN][1000 genomes]
rs7045761	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9314722	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944947	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987871	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10116424	UBQLN1	cis	cerebellum	SCAN
rs10116424	UBQLN1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:86289000-86308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
4	chr9:86291400-86314400	Weak transcription	Fetal Heart	heart
5	chr9:86292800-86308600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:86293600-86317000	Weak transcription	NHLF	lung
7	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:86294200-86305800	Weak transcription	Spleen	Spleen
9	chr9:86294200-86314200	Weak transcription	Gastric	stomach
10	chr9:86294200-86315600	Weak transcription	Right Ventricle	heart
11	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:86295000-86308800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:86295000-86313600	Weak transcription	Lung	lung
14	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
15	chr9:86296200-86316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:86296800-86306400	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:86296800-86314200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr9:86297000-86315600	Weak transcription	HMEC	breast
19	chr9:86297000-86315600	Weak transcription	HSMM	muscle
20	chr9:86297000-86320000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:86297200-86305400	Weak transcription	Psoas Muscle	Psoas
22	chr9:86297600-86305400	Weak transcription	Left Ventricle	heart
23	chr9:86297600-86305400	Weak transcription	Small Intestine	intestine
24	chr9:86297600-86310800	Weak transcription	Fetal Lung	lung
25	chr9:86297600-86314400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr9:86297600-86319800	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:86297600-86321200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:86297800-86305000	Weak transcription	Osteobl	bone
29	chr9:86297800-86311600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr9:86297800-86314800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr9:86297800-86315800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:86298000-86305400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:86298000-86307800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr9:86298000-86308000	Weak transcription	Primary B cells from cord blood	blood
35	chr9:86298000-86308200	Weak transcription	K562	blood
36	chr9:86298000-86313600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:86298000-86314200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr9:86298000-86315400	Weak transcription	HepG2	liver
39	chr9:86298000-86315600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr9:86298000-86316600	Weak transcription	Thymus	Thymus
41	chr9:86298000-86316800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:86298000-86320400	Weak transcription	Fetal Intestine Large	intestine
43	chr9:86298200-86311200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr9:86298200-86317000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:86298200-86317600	Weak transcription	Dnd41	blood
46	chr9:86298600-86320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:86298800-86305400	Weak transcription	Pancreas	Pancrea
48	chr9:86298800-86320800	Weak transcription	Fetal Thymus	thymus
49	chr9:86299600-86313600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:86299600-86319400	Weak transcription	Fetal Stomach	stomach

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