Variant report

Variant	rs6664147
Chromosome Location	chr1:227617519-227617520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr1:227617397-227617896	K562	blood:	n/a	n/a
2	REST	chr1:227617427-227617639	K562	blood:	n/a	n/a
3	JUN	chr1:227617265-227617754	HUVEC	blood vessel:	n/a	n/a
4	JUN	chr1:227617407-227617806	K562	blood:	n/a	n/a
5	FOS	chr1:227617133-227617871	HUVEC	blood vessel:	n/a	n/a
6	GATA2	chr1:227617188-227617820	HUVEC	blood vessel:	n/a	n/a
7	TBL1XR1	chr1:227617435-227617690	K562	blood:	n/a	n/a
8	EP300	chr1:227617305-227617836	K562	blood:	n/a	n/a
9	JUND	chr1:227617358-227617850	K562	blood:	n/a	n/a
10	FOXA1	chr1:227617307-227617744	T-47D	breast:	n/a	n/a
11	EP300	chr1:227617202-227617782	T-47D	breast:	n/a	n/a
12	FOXA1	chr1:227617396-227617783	T-47D	breast:	n/a	n/a
13	CUX1	chr1:227617439-227618068	K562	blood:	n/a	n/a
14	UBTF	chr1:227617242-227617724	K562	blood:	n/a	n/a
15	MAFK	chr1:227617485-227617686	K562	blood:	n/a	n/a
16	SP1	chr1:227616298-227617804	A549	lung:	n/a	n/a
17	NR3C1	chr1:227617286-227617647	A549	lung:	n/a	n/a
18	SP1	chr1:227616285-227617688	A549	lung:	n/a	n/a
19	TEAD4	chr1:227617108-227617829	K562	blood:	n/a	n/a
20	POLR2A	chr1:227616234-227617929	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr1:227617211-227617722	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr1:227615435-227618163	HUVEC	blood vessel:	n/a	n/a
23	GATA3	chr1:227616316-227617842	T-47D	breast:	n/a	chr1:227616399-227616406
24	MYC	chr1:227617276-227617663	K562	blood:	n/a	n/a
25	ZNF143	chr1:227617488-227617603	K562	blood:	n/a	n/a
26	MAX	chr1:227616216-227617961	A549	lung:	n/a	chr1:227616336-227616345
27	GATA3	chr1:227617313-227617792	T-47D	breast:	n/a	n/a
28	ZC3H11A	chr1:227617459-227617890	K562	blood:	n/a	n/a
29	FOXA2	chr1:227617313-227617816	A549	lung:	n/a	n/a
30	RCOR1	chr1:227617113-227618192	K562	blood:	n/a	n/a
31	NR3C1	chr1:227617119-227617697	A549	lung:	n/a	n/a
32	JUN	chr1:227616900-227618269	K562	blood:	n/a	n/a
33	EP300	chr1:227617211-227617835	T-47D	breast:	n/a	n/a
34	FOSL2	chr1:227617190-227617912	A549	lung:	n/a	n/a
35	TCF12	chr1:227616062-227617912	A549	lung:	n/a	n/a
36	RAD21	chr1:227617179-227617601	A549	lung:	n/a	n/a
37	TAL1	chr1:227617448-227617724	K562	blood:	n/a	n/a
38	ZMIZ1	chr1:227617507-227617714	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227502664..227506000-chr1:227614343..227617571,3	K562	blood:
2	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:
3	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:
4	chr1:227506036..227507932-chr1:227615818..227619997,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF678-1	chr1:227617106-227618736	ENSG00000234277.2

No data

Variant related genes	Relation type
ENSG00000242757	TF binding region
BTF3P9	TF binding region
ENSG00000228729	Chromatin interaction
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10799414	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10916130	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1495850	0.91[GIH][hapmap];1.00[JPT][hapmap]
rs3000801	0.85[GIH][hapmap]
rs3000803	1.00[ASW][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001353	chr1:227474785-227660691	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1003278	chr1:227563126-227678464	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv873243	chr1:227581017-227617519	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6664147	ZNF678	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227615200-227619400	Enhancers	Brain Hippocampus Middle	brain
2	chr1:227615200-227619600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:227615200-227621000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:227615400-227619400	Enhancers	Brain Anterior Caudate	brain
5	chr1:227615400-227623400	Enhancers	Brain Cingulate Gyrus	brain
6	chr1:227615600-227617800	Enhancers	Fetal Kidney	kidney
7	chr1:227615600-227621000	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr1:227616000-227617600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:227616000-227617800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr1:227616000-227618000	Enhancers	Fetal Stomach	stomach
11	chr1:227616000-227618000	Flanking Active TSS	A549	lung
12	chr1:227616000-227618200	Flanking Active TSS	HUVEC	blood vessel
13	chr1:227616000-227618400	Bivalent Enhancer	HepG2	liver
14	chr1:227616000-227618800	Enhancers	Brain Angular Gyrus	brain
15	chr1:227616000-227619200	Enhancers	Brain Substantia Nigra	brain
16	chr1:227616000-227622200	Enhancers	Fetal Muscle Leg	muscle
17	chr1:227616200-227618200	Enhancers	Small Intestine	intestine
18	chr1:227616200-227618200	Enhancers	Stomach Mucosa	stomach
19	chr1:227616200-227619400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr1:227616200-227619800	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr1:227616200-227620000	Enhancers	Fetal Muscle Trunk	muscle
22	chr1:227616400-227617600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr1:227616400-227617600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr1:227616400-227617600	Enhancers	Primary hematopoietic stem cells	blood
25	chr1:227616400-227617600	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:227616400-227617600	Enhancers	Fetal Intestine Small	intestine
27	chr1:227616400-227617600	Enhancers	Fetal Lung	lung
28	chr1:227616400-227617800	Enhancers	Rectal Smooth Muscle	rectum
29	chr1:227616400-227618200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:227616400-227618200	Enhancers	NHLF	lung
31	chr1:227616400-227618400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:227616400-227618400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr1:227616400-227618400	Enhancers	Right Atrium	heart
34	chr1:227616400-227618600	Enhancers	Left Ventricle	heart
35	chr1:227616400-227618600	Enhancers	NH-A	brain
36	chr1:227616400-227618800	Enhancers	Placenta	Placenta
37	chr1:227616400-227620000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr1:227616400-227621000	Enhancers	Lung	lung
39	chr1:227616600-227617600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:227616600-227617600	Enhancers	Fetal Heart	heart
41	chr1:227616600-227619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:227616600-227619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:227616600-227625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:227616800-227617600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:227616800-227617800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:227616800-227619400	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr1:227616800-227619400	Weak transcription	Hela-S3	cervix
48	chr1:227617000-227617600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:227617000-227617800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:227617000-227617800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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