Variant report

Variant	rs1076639
Chromosome Location	chr6:28290600-28290601
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	CEBPB	chr6:28290524-28290810	IMR90	lung:	n/a	chr6:28290678-28290689
2	JUND	chr6:28290550-28290775	HepG2	liver:	n/a	n/a
3	FOXA1	chr6:28290404-28290952	HepG2	liver:	n/a	n/a
4	CEBPB	chr6:28290505-28290864	HepG2	liver:	n/a	chr6:28290678-28290689
5	CEBPB	chr6:28290526-28290819	A549	lung:	n/a	chr6:28290678-28290689
6	FOXA2	chr6:28290522-28290870	HepG2	liver:	n/a	n/a
7	EP300	chr6:28290593-28290770	HepG2	liver:	n/a	n/a
8	CEBPD	chr6:28290547-28290784	HepG2	liver:	n/a	n/a
9	FOXA1	chr6:28290397-28290949	HepG2	liver:	n/a	n/a
10	USF2	chr6:28290511-28290783	HepG2	liver:	n/a	n/a
11	SP1	chr6:28290489-28290967	HepG2	liver:	n/a	n/a
12	BHLHE40	chr6:28290490-28290805	HepG2	liver:	n/a	n/a
13	CEBPB	chr6:28290386-28290851	HepG2	liver:	n/a	chr6:28290678-28290689
14	BHLHE40	chr6:28290493-28290853	HepG2	liver:	n/a	n/a
15	CEBPB	chr6:28290542-28290824	Hela-S3	cervix:	n/a	chr6:28290678-28290689
16	FOXA1	chr6:28290414-28290852	HepG2	liver:	n/a	n/a
17	ARID3A	chr6:28290515-28290788	HepG2	liver:	n/a	n/a
18	TEAD4	chr6:28290397-28290918	HepG2	liver:	n/a	n/a
19	USF1	chr6:28290559-28290754	HepG2	liver:	n/a	chr6:28290668-28290679
20	CEBPB	chr6:28290297-28290872	HepG2	liver:	n/a	chr6:28290678-28290689
21	EP300	chr6:28290459-28290881	HepG2	liver:	n/a	n/a
22	FOXA1	chr6:28290495-28290888	HepG2	liver:	n/a	n/a
23	BHLHE40	chr6:28290502-28290854	HepG2	liver:	n/a	n/a
24	CEBPB	chr6:28290582-28290782	HepG2	liver:	n/a	chr6:28290678-28290689
25	CEBPB	chr6:28290512-28290782	K562	blood:	n/a	chr6:28290678-28290689
26	CEBPB	chr6:28290517-28290908	MCF-7	breast:	n/a	chr6:28290678-28290689

No.	Distal block	Cell Line	Cell type
1	chr6:28289244..28291635-chr6:28299932..28302110,2	MCF-7	breast:
2	chr6:28288486..28291463-chr6:28293519..28295323,2	K562	blood:
3	chr6:28281200..28284924-chr6:28289065..28292211,3	K562	blood:

Variant related genes	Relation type
ENSG00000270326	TF binding region
ENSG00000235109	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10456362	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11755032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11965538	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13200462	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1339899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1419183	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1679709	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1679732	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1778507	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1778508	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1778511	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1936365	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs213239	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213241	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213243	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213244	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2743554	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2743555	0.80[ASN][1000 genomes]
rs2799077	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2799079	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs68141011	0.81[ASN][1000 genomes]
rs6901575	1.00[JPT][hapmap]
rs6920512	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs73742521	0.94[EUR][1000 genomes]
rs853676	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853678	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853679	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853681	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853682	0.87[ASN][1000 genomes]
rs853685	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs853687	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs853688	0.91[ASN][1000 genomes]
rs853694	0.86[ASN][1000 genomes]
rs9295765	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9366717	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9393908	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs9461446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9461448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9461449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9468322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9468342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468345	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9986596	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1076639	ZSCAN31	cis	Nerve Tibial	GTEx
rs1076639	ZSCAN31	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28250000-28293800	Weak transcription	Gastric	stomach
2	chr6:28255200-28293800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:28268800-28293400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:28269200-28291600	Weak transcription	Right Ventricle	heart
5	chr6:28270000-28291400	Weak transcription	Ovary	ovary
6	chr6:28270000-28291600	Weak transcription	Brain Anterior Caudate	brain
7	chr6:28270000-28291600	Weak transcription	Fetal Brain Female	brain
8	chr6:28270000-28293400	Weak transcription	Brain Angular Gyrus	brain
9	chr6:28271200-28293800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:28271400-28293400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr6:28272400-28291800	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:28272400-28293200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:28272600-28292000	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:28272600-28292600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:28272600-28292600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:28273000-28291600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:28279400-28290600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:28279400-28293800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:28281200-28290800	Weak transcription	Fetal Stomach	stomach
20	chr6:28281200-28290800	Weak transcription	Left Ventricle	heart
21	chr6:28281200-28291600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:28281200-28291600	Weak transcription	Pancreas	Pancrea
23	chr6:28281200-28293600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:28288800-28293600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr6:28289200-28293600	Weak transcription	Brain Substantia Nigra	brain
27	chr6:28289600-28292600	Strong transcription	Stomach Smooth Muscle	stomach
28	chr6:28289600-28293200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:28289800-28291400	Enhancers	HepG2	liver
30	chr6:28289800-28292200	ZNF genes & repeats	Aorta	Aorta
31	chr6:28290000-28293600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:28290200-28293600	Weak transcription	Colonic Mucosa	Colon
33	chr6:28290400-28290600	Enhancers	Lung	lung
34	chr6:28290400-28291200	Enhancers	Liver	Liver
35	chr6:28290400-28291600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:28290400-28291600	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:28290600-28291600	Weak transcription	Lung	lung
38	chr6:28290600-28295800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum

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