Variant report

Variant	rs2296073
Chromosome Location	chr9:116061628-116061629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:116061614-116061664	Hepatocyte	liver:	n/a
2	chr9:116061614-116061664	HPAEpiC	pulmonary alveolar:	n/a
3	chr9:116061614-116061664	PFSK-1	brain:	n/a
4	chr9:116061614-116061664	HEK293	kidney:	embryo
5	chr9:116061614-116061664	SK-N-SH_RA	brain:	n/a
6	chr9:116061614-116061664	HCPEpiC	choroid plexus:	n/a
7	chr9:116061614-116061664	NHDF-neo	bronchial:	n/a
8	chr9:116061614-116061664	AG04449	skin:	fetal
9	chr9:116061614-116061664	SK-N-SH	brain:	n/a
10	chr9:116061614-116061664	HepG2	liver:	n/a
11	chr9:116061614-116061664	NH-A	brain:	n/a
12	chr9:116061614-116061664	NT2-D1	testis:	n/a
13	chr9:116061614-116061664	GM19239	blood:	n/a
14	chr9:116061614-116061664	HUVEC	blood vessel:	n/a
15	chr9:116061614-116061664	PANC-1	pancreas:	n/a
16	chr9:116061614-116061664	SKMC	muscle:	n/a
17	chr9:116061614-116061664	T-47D	breast:	n/a
18	chr9:116061614-116061664	ECC-1	luminal epithelium:	n/a
19	chr9:116061614-116061664	AoSMC	blood vessel:	n/a
20	chr9:116061614-116061664	MCF-7	breast:	n/a
21	chr9:116061614-116061664	A549	lung:	n/a
22	chr9:116061614-116061664	BJ	skin:	n/a
23	chr9:116061614-116061664	GM12891	blood:	n/a
24	chr9:116061614-116061664	K562	blood:	n/a
25	chr9:116061614-116061664	U87	brain:	n/a
26	chr9:116061614-116061664	CMK	blood:	n/a
27	chr9:116061614-116061664	ProgFib	skin:	n/a
28	chr9:116061614-116061664	AG09319	gingival:	n/a
29	chr9:116061614-116061664	HIPEpiC	eye:	n/a
30	chr9:116061614-116061664	SK-N-MC	brain:	n/a
31	chr9:116061614-116061664	NHBE	bronchial:	n/a
32	chr9:116061614-116061664	SAEC	small airway:	n/a
33	chr9:116061614-116061664	HNPCEpiC	eye:	n/a
34	chr9:116061614-116061664	HCT-116	colon:	n/a
35	chr9:116061614-116061664	HRCEpiC	kidney:	n/a
36	chr9:116061614-116061664	Hela-S3	cervix:	n/a
37	chr9:116061614-116061664	GM12878	blood:	n/a
38	chr9:116061614-116061664	HCF	heart:	n/a
39	chr9:116061614-116061664	AG04450	lung:	fetal
40	chr9:116061614-116061664	IMR90	lung:	fetal
41	chr9:116061614-116061664	Jurkat	blood:	n/a
42	chr9:116061614-116061664	GM12892	blood:	n/a
43	chr9:116061614-116061664	BE2_C	brain:	n/a
44	chr9:116061614-116061664	NB4	blood:	n/a
45	chr9:116061614-116061664	LNCaP	prostate:	n/a
46	chr9:116061614-116061664	HL-60	blood:	n/a
47	chr9:116061614-116061664	AG09309	skin:	n/a
48	chr9:116061614-116061664	PrEC	prostate:	n/a
49	chr9:116061614-116061664	AG10803	skin:	n/a
50	chr9:116061614-116061664	RPTEC	kidney:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:116039888..116041521-chr9:116060320..116062417,2	K562	blood:
2	chr9:116060077..116063011-chr9:116109868..116112387,2	MCF-7	breast:
3	chr9:116060084..116062548-chr9:116172614..116174498,2	K562	blood:

No data

Variant related genes	Relation type
RNF183	CpG island
ENSG00000119411	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000148229	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10114327	0.85[AFR][1000 genomes]
rs10116039	0.81[MKK][hapmap]
rs10117451	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10124515	0.86[CHB][hapmap]
rs10513189	0.82[CHB][hapmap]
rs10739390	0.82[CHB][hapmap]
rs10759636	0.82[CHB][hapmap]
rs10759637	0.82[CHB][hapmap]
rs10759638	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10759640	0.84[AFR][1000 genomes]
rs10817474	0.86[CEU][hapmap];0.84[TSI][hapmap]
rs10817475	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs10817481	0.83[AFR][1000 genomes]
rs10981710	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10981715	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10981762	0.85[CHB][hapmap];0.81[CHD][hapmap]
rs11552582	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11789755	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12236683	0.83[EUR][1000 genomes]
rs12343629	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1323466	0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs2093691	0.85[ASW][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.93[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap]
rs28440160	0.80[ASN][1000 genomes]
rs3750532	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3750533	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750534	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3750535	1.00[CEU][hapmap]
rs3810921	0.93[LWK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4560868	0.82[CHB][hapmap]
rs4979223	0.82[CHB][hapmap]
rs4979226	0.82[CHB][hapmap]
rs4979231	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4979232	0.88[CEU][hapmap];0.82[CHB][hapmap];0.88[TSI][hapmap]
rs4979233	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6477998	0.82[CHB][hapmap]
rs6478000	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6478002	0.87[AFR][1000 genomes]
rs6478003	0.81[AFR][1000 genomes]
rs6478006	0.86[CHB][hapmap]
rs7022397	0.81[CHB][hapmap]
rs7025371	0.84[AFR][1000 genomes]
rs7027833	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041572	0.87[AFR][1000 genomes]
rs7041615	0.82[CHB][hapmap]
rs7847295	0.80[ASN][1000 genomes]
rs7849326	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7849513	0.90[CHB][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs7850264	0.82[AFR][1000 genomes]
rs7850357	0.82[CHB][hapmap]
rs7851395	0.82[CHB][hapmap]
rs7860625	0.91[CHB][hapmap]
rs7863921	0.84[AFR][1000 genomes]
rs7864788	0.87[AFR][1000 genomes]
rs7868271	0.91[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]
rs7873862	0.82[CHB][hapmap]
rs9299214	1.00[CEU][hapmap];0.81[JPT][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription 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 target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs2296073	CDC26	cis	parietal	SCAN
rs2296073	CDC26	cis	Adipose Subcutaneous	GTEx
rs2296073	CDC26	cis	Skin Sun Exposed Lower leg	GTEx
rs2296073	CDC26	cis	cerebellum	SCAN
rs2296073	PRPF4	cis	Thyroid	GTEx
rs2296073	CDC26	cis	Nerve Tibial	GTEx
rs2296073	CDC26	cis	Muscle Skeletal	GTEx
rs2296073	CDC26	cis	Esophagus Muscularis	GTEx
rs2296073	CDC26	cis	Thyroid	GTEx
rs2296073	CDC26	cis	Artery Tibial	GTEx
rs2296073	CDC26	cis	Heart Left Ventricle	GTEx
rs2296073	CDC26	cis	Whole Blood	GTEx
rs2296073	ZNF618	cis	cerebellum	SCAN
rs2296073	BSPRY	cis	Heart Left Ventricle	GTEx
rs2296073	CDC26	cis	Esophagus Mucosa	GTEx
rs2296073	CDC26	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116050000-116062000	Weak transcription	Stomach Mucosa	stomach
2	chr9:116054200-116065000	Weak transcription	Fetal Kidney	kidney
3	chr9:116054600-116065200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:116054800-116062200	Weak transcription	Colonic Mucosa	Colon
5	chr9:116054800-116062200	Weak transcription	Pancreas	Pancrea
6	chr9:116054800-116065200	Weak transcription	Esophagus	oesophagus
7	chr9:116055000-116063800	Weak transcription	Spleen	Spleen
8	chr9:116055200-116085200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:116055600-116062200	Weak transcription	A549	lung
10	chr9:116055800-116061800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:116055800-116062000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:116056000-116062000	Weak transcription	Gastric	stomach
13	chr9:116056000-116087000	Weak transcription	Thymus	Thymus
14	chr9:116056200-116062200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:116056200-116062200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:116056200-116062200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr9:116056200-116062200	Weak transcription	HUVEC	blood vessel
18	chr9:116056200-116062600	Weak transcription	Primary B cells from cord blood	blood
19	chr9:116056400-116061800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:116056400-116064600	Weak transcription	Fetal Intestine Large	intestine
21	chr9:116056600-116062200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:116056600-116062200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:116056600-116062200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr9:116056600-116062400	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr9:116056600-116065400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr9:116056800-116062200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:116056800-116062200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr9:116056800-116062600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr9:116056800-116063200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:116056800-116065000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr9:116056800-116065200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:116057400-116062200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:116058400-116064600	Weak transcription	HepG2	liver
34	chr9:116059200-116062000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr9:116061000-116062400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr9:116061000-116064800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr9:116061400-116065200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr9:116061600-116062000	Bivalent Enhancer	K562	blood
39	chr9:116061600-116062600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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