Variant report

Variant	rs7821559
Chromosome Location	chr8:9413300-9413301
allele	A/G
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	YY1	chr8:9412990-9414239	ECC-1	luminal epithelium:	n/a	n/a
2	RFX5	chr8:9413100-9413504	K562	blood:	n/a	chr8:9413372-9413381
3	SP1	chr8:9413052-9413625	GM12878	blood:	n/a	chr8:9413270-9413284 chr8:9413270-9413279 chr8:9413269-9413281 chr8:9413311-9413322 chr8:9413269-9413281 chr8:9413269-9413280 chr8:9413271-9413280 chr8:9413362-9413383 chr8:9413270-9413279
4	POLR2A	chr8:9412825-9413881	PFSK-1	brain:	n/a	n/a
5	MXI1	chr8:9413007-9414438	HepG2	liver:	n/a	n/a
6	MAX	chr8:9412969-9413618	K562	blood:	n/a	n/a
7	POLR2A	chr8:9413010-9413824	A549	lung:	n/a	n/a
8	ZMIZ1	chr8:9412389-9413608	K562	blood:	n/a	n/a
9	POLR2A	chr8:9412691-9414855	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3A	chr8:9412948-9414684	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr8:9412973-9413830	A549	lung:	n/a	n/a
12	IRF1	chr8:9412786-9413544	K562	blood:	n/a	chr8:9413267-9413281
13	CHD1	chr8:9412765-9414770	IMR90	lung:	n/a	n/a
14	MYBL2	chr8:9412996-9413625	HepG2	liver:	n/a	n/a
15	GTF2B	chr8:9413069-9413448	K562	blood:	n/a	n/a
16	MAFK	chr8:9412985-9413477	K562	blood:	n/a	chr8:9413305-9413320
17	TBP	chr8:9412960-9414406	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOXP2	chr8:9413008-9413874	SK-N-MC	brain:	n/a	n/a
19	TAF1	chr8:9412938-9414155	H1-hESC	embryonic stem cell:	n/a	n/a
20	BHLHE40	chr8:9413099-9413550	GM12878	blood:	n/a	n/a
21	TAL1	chr8:9413010-9413334	K562	blood:	n/a	n/a
22	TBP	chr8:9413013-9413573	GM12878	blood:	n/a	n/a
23	POLR2A	chr8:9412948-9413632	Hela-S3	cervix:	n/a	n/a
24	NFYB	chr8:9412925-9413562	Hela-S3	cervix:	n/a	chr8:9413369-9413384 chr8:9413370-9413384 chr8:9413369-9413384 chr8:9413372-9413382
25	SIX5	chr8:9413290-9413557	A549	lung:	n/a	n/a
26	GABPA	chr8:9413050-9414170	K562	blood:	n/a	n/a
27	POLR2A	chr8:9412869-9414414	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr8:9413044-9414454	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr8:9413033-9414138	GM12878	blood:	n/a	n/a
30	ZNF143	chr8:9413045-9414119	GM12878	blood:	n/a	chr8:9413400-9413410
31	POLR2A	chr8:9412966-9414249	GM12892	blood:	n/a	n/a
32	CREB1	chr8:9412963-9414251	GM12878	blood:	n/a	n/a
33	ZNF263	chr8:9412979-9414313	HEK293-T-REx	kidney:	n/a	chr8:9413854-9413875
34	TAF1	chr8:9412878-9413667	K562	blood:	n/a	n/a
35	SRF	chr8:9413282-9413663	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAZ	chr8:9413002-9414598	IMR90	lung:	n/a	n/a
37	GABPA	chr8:9413176-9413638	GM12878	blood:	n/a	n/a
38	POLR2A	chr8:9412935-9413653	HCT-116	colon:	n/a	n/a
39	YY1	chr8:9413232-9413614	A549	lung:	n/a	n/a
40	CREB1	chr8:9413002-9413810	ECC-1	luminal epithelium:	n/a	n/a
41	GABPA	chr8:9412813-9414295	A549	lung:	n/a	n/a
42	POLR2A	chr8:9412812-9414322	HUVEC	blood vessel:	n/a	n/a
43	RELA	chr8:9413004-9413703	GM19099	blood:	n/a	n/a
44	YY1	chr8:9413163-9414221	GM12891	blood:	n/a	n/a
45	TCF12	chr8:9413080-9413699	GM12878	blood:	n/a	chr8:9413089-9413096
46	ETS1	chr8:9412982-9413732	A549	lung:	n/a	chr8:9413171-9413188 chr8:9413398-9413409 chr8:9413171-9413188 chr8:9413170-9413183 chr8:9413171-9413185
47	CHD2	chr8:9412966-9413945	GM12878	blood:	n/a	n/a
48	MAX	chr8:9413043-9413828	A549	lung:	n/a	n/a
49	NFYB	chr8:9412950-9413631	K562	blood:	n/a	chr8:9413369-9413384 chr8:9413370-9413384 chr8:9413369-9413384 chr8:9413372-9413382
50	HDAC2	chr8:9413259-9413661	HepG2	liver:	n/a	chr8:9413312-9413326

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9412503..9413441-chr8:55013581..55014482,2	Hela-S3	cervix:
2	chr19:50370371..50371012-chr8:9413199..9414102,2	Hela-S3	cervix:

Variant related genes	Relation type
TNKS	TF binding region
ENSG00000120992	Chromatin interaction
ENSG00000039650	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10087012	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10087166	0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10088969	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10098758	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10101953	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10102030	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs10103426	0.86[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10111980	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10503380	0.84[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs10903314	0.86[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs11779335	0.92[GIH][hapmap]
rs11984585	0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11985349	0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11995920	0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12541409	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12543534	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12545912	0.94[GIH][hapmap]
rs12548306	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12674762	0.84[CHD][hapmap];0.94[GIH][hapmap];0.93[MEX][hapmap]
rs12675476	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12675511	0.91[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12676898	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12679892	0.82[CHB][hapmap]
rs12681719	0.91[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13271097	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13273033	0.94[GIH][hapmap];1.00[MEX][hapmap]
rs17150237	0.87[ASW][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28622033	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28668310	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33945943	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34206126	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34324628	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34790717	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4128199	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4240626	0.86[CHD][hapmap];0.94[GIH][hapmap];0.94[MEX][hapmap]
rs4398920	0.86[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs4840427	0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs4841173	0.85[AMR][1000 genomes]
rs4841174	0.87[AMR][1000 genomes]
rs4841175	0.80[EUR][1000 genomes]
rs4841179	0.97[GIH][hapmap];0.94[MEX][hapmap]
rs4841212	0.94[GIH][hapmap]
rs57453266	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58238328	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61551896	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62493868	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601331	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601332	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6601333	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601334	0.84[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601335	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6601336	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6601337	0.80[EUR][1000 genomes]
rs66516712	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67706102	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6980831	0.86[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6985140	0.81[GIH][hapmap]
rs6986386	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6989126	0.80[EUR][1000 genomes]
rs6990097	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]
rs6990590	0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7013500	0.84[ASN][1000 genomes]
rs73193784	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7462910	0.92[GIH][hapmap]
rs7814014	0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs7815817	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7822548	0.84[AMR][1000 genomes]
rs7832096	0.97[GIH][hapmap];0.94[MEX][hapmap]
rs7834823	0.84[CHD][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap]
rs7844450	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7846140	0.81[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9329202	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9329203	0.80[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9644677	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7821559	TNKS	cis	parietal	SCAN
rs7821559	PRSS55	cis	cerebellum	SCAN
rs7821559	TNKS	cis	cerebellum	SCAN
rs7821559	DEFB134	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9412200-9413400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:9412200-9414600	Active TSS	Fetal Brain Female	brain
3	chr8:9412200-9415200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr8:9412200-9415400	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr8:9412200-9416800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:9412400-9413600	Active TSS	HepG2	liver
7	chr8:9412400-9414400	Active TSS	A549	lung
8	chr8:9412400-9414600	Active TSS	iPS-18 Cell Line	embryonic stem cell
9	chr8:9412400-9414600	Active TSS	NH-A	brain
10	chr8:9412400-9415000	Active TSS	HSMM	muscle
11	chr8:9412400-9415400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr8:9412400-9415400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr8:9412600-9414000	Active TSS	Stomach Smooth Muscle	stomach
14	chr8:9412600-9414600	Active TSS	K562	blood
15	chr8:9412600-9415000	Active TSS	H1 Cell Line	embryonic stem cell
16	chr8:9412600-9415400	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr8:9412600-9415400	Active TSS	HMEC	breast
18	chr8:9412600-9415600	Active TSS	NHLF	lung
19	chr8:9412600-9415800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:9412600-9415800	Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr8:9412600-9416200	Active TSS	NHDF-Ad	bronchial
22	chr8:9412600-9417000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr8:9412800-9413600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr8:9412800-9413600	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr8:9412800-9413800	Active TSS	Fetal Muscle Trunk	muscle
26	chr8:9412800-9414200	Active TSS	Brain Hippocampus Middle	brain
27	chr8:9412800-9414200	Active TSS	Fetal Brain Male	brain
28	chr8:9412800-9414200	Active TSS	Rectal Smooth Muscle	rectum
29	chr8:9412800-9414200	Active TSS	Thymus	Thymus
30	chr8:9412800-9414400	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr8:9412800-9414400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr8:9412800-9414400	Active TSS	Brain Angular Gyrus	brain
33	chr8:9412800-9414400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr8:9412800-9414400	Active TSS	Fetal Kidney	kidney
35	chr8:9412800-9414600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr8:9412800-9414600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr8:9412800-9414600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:9412800-9414600	Active TSS	Aorta	Aorta
39	chr8:9412800-9414600	Active TSS	Fetal Intestine Large	intestine
40	chr8:9412800-9414600	Active TSS	Fetal Lung	lung
41	chr8:9412800-9414800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr8:9412800-9414800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr8:9412800-9414800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr8:9412800-9414800	Active TSS	Colonic Mucosa	Colon
45	chr8:9412800-9414800	Active TSS	Ovary	ovary
46	chr8:9412800-9414800	Active TSS	Psoas Muscle	Psoas
47	chr8:9412800-9414800	Active TSS	Right Ventricle	heart
48	chr8:9412800-9415000	Active TSS	H9 Cell Line	embryonic stem cell
49	chr8:9412800-9415000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr8:9412800-9415000	Active TSS	Brain Substantia Nigra	brain

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