Variant report

Variant	rs6990097
Chromosome Location	chr8:9412857-9412858
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	chr8:9412825-9413881	PFSK-1	brain:	n/a	n/a
2	ZMIZ1	chr8:9412389-9413608	K562	blood:	n/a	n/a
3	POLR2A	chr8:9412691-9414855	H1-hESC	embryonic stem cell:	n/a	n/a
4	IRF1	chr8:9412786-9413544	K562	blood:	n/a	chr8:9413267-9413281
5	CHD1	chr8:9412765-9414770	IMR90	lung:	n/a	n/a
6	GABPA	chr8:9412813-9414295	A549	lung:	n/a	n/a
7	POLR2A	chr8:9412812-9414322	HUVEC	blood vessel:	n/a	n/a
8	REST	chr8:9412800-9413694	A549	lung:	n/a	n/a
9	RFX5	chr8:9412580-9414144	SK-N-SH	brain:	n/a	chr8:9413372-9413381
10	POLR2A	chr8:9412813-9413752	PFSK-1	brain:	n/a	n/a
11	NR2F2	chr8:9412846-9413595	K562	blood:	n/a	n/a
12	RFX5	chr8:9412852-9413635	Hela-S3	cervix:	n/a	chr8:9413372-9413381
13	POLR2A	chr8:9412168-9414392	Hela-S3	cervix:	n/a	n/a
14	MYC	chr8:9412840-9413392	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr8:9412563-9413525	Hela-S3	cervix:	n/a	chr8:9412738-9412749
16	TCF12	chr8:9412803-9413906	ECC-1	luminal epithelium:	n/a	chr8:9412883-9412890 chr8:9413089-9413096
17	POLR2A	chr8:9412210-9414428	K562	blood:	n/a	n/a
18	CEBPB	chr8:9412597-9412874	K562	blood:	n/a	chr8:9412738-9412749
19	MAX	chr8:9412846-9414230	A549	lung:	n/a	n/a
20	TBP	chr8:9412238-9413674	K562	blood:	n/a	n/a
21	MYC	chr8:9412198-9413703	K562	blood:	n/a	n/a
22	POLR2A	chr8:9412855-9413633	K562	blood:	n/a	n/a
23	GATA3	chr8:9412835-9413028	SH-SY5Y	brain:	n/a	n/a
24	POLR2A	chr8:9412748-9414570	GM12891	blood:	n/a	n/a
25	HCFC1	chr8:9412542-9414660	Hela-S3	cervix:	n/a	n/a
26	REST	chr8:9412828-9414272	HL-60	blood:	n/a	n/a
27	POLR2A	chr8:9412704-9414676	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr8:9412776-9413572	HepG2	liver:	n/a	n/a
29	E2F4	chr8:9412561-9413571	MCF10A-Er-Src	breast:	n/a	chr8:9413211-9413220
30	CREB1	chr8:9412851-9413829	GM12878	blood:	n/a	n/a
31	TCF12	chr8:9412855-9414131	A549	lung:	n/a	chr8:9412883-9412890 chr8:9413089-9413096
32	SIN3AK20	chr8:9412794-9414063	MCF-7	breast:	n/a	n/a
33	KAP1	chr8:9412797-9413492	U2OS	brain:	n/a	n/a
34	MXI1	chr8:9412734-9413663	Hela-S3	cervix:	n/a	n/a
35	GABPA	chr8:9412794-9414230	MCF-7	breast:	n/a	n/a
36	PML	chr8:9412853-9413416	K562	blood:	n/a	n/a
37	MXI1	chr8:9411917-9414938	SK-N-SH	brain:	n/a	n/a
38	TBL1XR1	chr8:9412354-9413581	K562	blood:	n/a	n/a
39	POLR2A	chr8:9412787-9413873	K562	blood:	n/a	n/a
40	RCOR1	chr8:9412760-9414407	Hela-S3	cervix:	n/a	n/a
41	CEBPB	chr8:9412597-9412862	HepG2	liver:	n/a	chr8:9412738-9412749
42	TBP	chr8:9412757-9413508	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr8:9412796-9414092	U87	brain:	n/a	n/a
44	MXI1	chr8:9412834-9414181	GM12878	blood:	n/a	n/a
45	UBTF	chr8:9412290-9414214	K562	blood:	n/a	n/a
46	POLR2A	chr8:9412796-9414237	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9412503..9413441-chr8:55013581..55014482,2	Hela-S3	cervix:

Variant related genes	Relation type
TNKS	TF binding region
ENSG00000120992	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10087012	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10087166	0.82[CHB][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10088969	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10098758	0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10101953	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs10102030	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs10103426	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10111980	0.82[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10503380	0.90[JPT][hapmap]
rs10903314	0.80[CHD][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs11984585	0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11985349	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11995920	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12541409	0.81[AMR][1000 genomes]
rs12543534	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12545912	0.82[GIH][hapmap]
rs12548306	0.88[ASN][1000 genomes]
rs12674762	0.82[GIH][hapmap];0.81[MEX][hapmap]
rs12675476	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12675511	0.91[CHB][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12676898	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12679892	0.82[CHB][hapmap]
rs12681719	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs13271097	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13273033	0.82[GIH][hapmap];0.88[MEX][hapmap]
rs17150237	0.87[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28622033	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28668310	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs33945943	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34206126	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34324628	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34790717	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4128199	0.84[AMR][1000 genomes]
rs4240626	0.82[GIH][hapmap];0.83[MEX][hapmap]
rs4398920	0.81[GIH][hapmap]
rs4841173	0.81[AMR][1000 genomes]
rs4841174	0.82[AMR][1000 genomes]
rs4841179	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs4841212	0.82[GIH][hapmap]
rs57453266	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs58238328	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61551896	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62493868	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6601330	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6601331	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6601332	0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6601333	0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6601334	0.84[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6601335	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6601336	0.82[AMR][1000 genomes]
rs66516712	0.86[ASN][1000 genomes]
rs67706102	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6980831	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6986386	0.82[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6990590	0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7013500	0.83[ASN][1000 genomes]
rs73193784	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7814014	0.84[GIH][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs7815817	0.82[AMR][1000 genomes]
rs7821559	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7832096	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs7834823	0.82[GIH][hapmap]
rs7844450	0.80[ASN][1000 genomes]
rs7846140	0.81[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9329202	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9329203	0.80[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9644677	0.95[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9650638	0.82[CHB][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	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1033031	chr8:9310266-9418941	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6990097	DEFB134	cis	cerebellum	SCAN
rs6990097	TNKS	cis	parietal	SCAN
rs6990097	TNKS	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9412200-9413000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr8:9412200-9413000	Enhancers	Brain Cingulate Gyrus	brain
3	chr8:9412200-9413000	Flanking Active TSS	Brain Germinal Matrix	brain
4	chr8:9412200-9413000	Enhancers	Placenta	Placenta
5	chr8:9412200-9413000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr8:9412200-9413000	Flanking Active TSS	Hela-S3	cervix
7	chr8:9412200-9413200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
8	chr8:9412200-9413400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr8:9412200-9414600	Active TSS	Fetal Brain Female	brain
10	chr8:9412200-9415200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr8:9412200-9415400	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr8:9412200-9416800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr8:9412400-9413000	Enhancers	Fetal Heart	heart
14	chr8:9412400-9413600	Active TSS	HepG2	liver
15	chr8:9412400-9414400	Active TSS	A549	lung
16	chr8:9412400-9414600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr8:9412400-9414600	Active TSS	NH-A	brain
18	chr8:9412400-9415000	Active TSS	HSMM	muscle
19	chr8:9412400-9415400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr8:9412400-9415400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr8:9412600-9413000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr8:9412600-9413000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr8:9412600-9413000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr8:9412600-9413000	Enhancers	Stomach Mucosa	stomach
25	chr8:9412600-9413000	Flanking Active TSS	HUVEC	blood vessel
26	chr8:9412600-9413000	Flanking Active TSS	NHEK	skin
27	chr8:9412600-9413200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
28	chr8:9412600-9413200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr8:9412600-9413200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr8:9412600-9413200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr8:9412600-9413200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr8:9412600-9413200	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr8:9412600-9413200	Flanking Active TSS	Dnd41	blood
34	chr8:9412600-9414000	Active TSS	Stomach Smooth Muscle	stomach
35	chr8:9412600-9414600	Active TSS	K562	blood
36	chr8:9412600-9415000	Active TSS	H1 Cell Line	embryonic stem cell
37	chr8:9412600-9415400	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr8:9412600-9415400	Active TSS	HMEC	breast
39	chr8:9412600-9415600	Active TSS	NHLF	lung
40	chr8:9412600-9415800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr8:9412600-9415800	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr8:9412600-9416200	Active TSS	NHDF-Ad	bronchial
43	chr8:9412600-9417000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr8:9412800-9413000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr8:9412800-9413000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr8:9412800-9413000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr8:9412800-9413000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr8:9412800-9413000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr8:9412800-9413000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
50	chr8:9412800-9413000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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