Variant report

Variant	rs3014301
Chromosome Location	chr1:227617699-227617700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 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	JUN	chr1:227617265-227617754	HUVEC	blood vessel:	n/a	n/a
3	JUN	chr1:227617407-227617806	K562	blood:	n/a	n/a
4	FOS	chr1:227617133-227617871	HUVEC	blood vessel:	n/a	n/a
5	GATA2	chr1:227617188-227617820	HUVEC	blood vessel:	n/a	n/a
6	EP300	chr1:227617305-227617836	K562	blood:	n/a	n/a
7	JUND	chr1:227617358-227617850	K562	blood:	n/a	n/a
8	FOXA1	chr1:227617307-227617744	T-47D	breast:	n/a	n/a
9	EP300	chr1:227617202-227617782	T-47D	breast:	n/a	n/a
10	FOXA1	chr1:227617396-227617783	T-47D	breast:	n/a	n/a
11	CUX1	chr1:227617439-227618068	K562	blood:	n/a	n/a
12	CHD2	chr1:227617564-227617908	K562	blood:	n/a	n/a
13	UBTF	chr1:227617242-227617724	K562	blood:	n/a	n/a
14	SP1	chr1:227616298-227617804	A549	lung:	n/a	n/a
15	TBL1XR1	chr1:227617577-227617754	K562	blood:	n/a	n/a
16	TEAD4	chr1:227617108-227617829	K562	blood:	n/a	n/a
17	POLR2A	chr1:227616234-227617929	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr1:227617211-227617722	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr1:227615435-227618163	HUVEC	blood vessel:	n/a	n/a
20	GATA3	chr1:227616316-227617842	T-47D	breast:	n/a	chr1:227616399-227616406
21	MAX	chr1:227616216-227617961	A549	lung:	n/a	chr1:227616336-227616345
22	GATA3	chr1:227617313-227617792	T-47D	breast:	n/a	n/a
23	ZC3H11A	chr1:227617459-227617890	K562	blood:	n/a	n/a
24	FOXA2	chr1:227617313-227617816	A549	lung:	n/a	n/a
25	RCOR1	chr1:227617113-227618192	K562	blood:	n/a	n/a
26	JUN	chr1:227616900-227618269	K562	blood:	n/a	n/a
27	EP300	chr1:227617211-227617835	T-47D	breast:	n/a	n/a
28	FOSL2	chr1:227617190-227617912	A549	lung:	n/a	n/a
29	TCF12	chr1:227616062-227617912	A549	lung:	n/a	n/a
30	TAL1	chr1:227617448-227617724	K562	blood:	n/a	n/a
31	ZMIZ1	chr1:227617507-227617714	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:227504042..227507688-chr1:227616722..227620233,4	K562	blood:
2	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:
3	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: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10082258	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12729548	0.84[AMR][1000 genomes]
rs3000775	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs3000778	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000779	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000781	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000782	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3000783	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000784	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000785	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3000786	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000787	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs3000788	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000789	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000791	0.87[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3000792	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000793	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3000794	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3000795	0.81[AMR][1000 genomes]
rs3000796	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3000797	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3000798	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3000804	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3000806	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000807	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000809	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3000810	1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3000811	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014273	1.00[CEU][hapmap]
rs3014275	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3014277	0.86[ASN][1000 genomes]
rs3014278	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3014279	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs3014280	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap]
rs3014287	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014288	1.00[CEU][hapmap];0.80[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014290	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3014291	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3014292	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3014293	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3014295	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3014296	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3014297	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014298	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3014300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3122560	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3122561	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3125124	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4468130	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4521965	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs4570389	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6667621	0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6702589	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs9426519	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9426520	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9426521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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

No data

Chromatin state (count:75 , 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	chr1:227616000-227617800	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr1:227616000-227618000	Enhancers	Fetal Stomach	stomach
10	chr1:227616000-227618000	Flanking Active TSS	A549	lung
11	chr1:227616000-227618200	Flanking Active TSS	HUVEC	blood vessel
12	chr1:227616000-227618400	Bivalent Enhancer	HepG2	liver
13	chr1:227616000-227618800	Enhancers	Brain Angular Gyrus	brain
14	chr1:227616000-227619200	Enhancers	Brain Substantia Nigra	brain
15	chr1:227616000-227622200	Enhancers	Fetal Muscle Leg	muscle
16	chr1:227616200-227618200	Enhancers	Small Intestine	intestine
17	chr1:227616200-227618200	Enhancers	Stomach Mucosa	stomach
18	chr1:227616200-227619400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr1:227616200-227619800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:227616200-227620000	Enhancers	Fetal Muscle Trunk	muscle
21	chr1:227616400-227617800	Enhancers	Rectal Smooth Muscle	rectum
22	chr1:227616400-227618200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:227616400-227618200	Enhancers	NHLF	lung
24	chr1:227616400-227618400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:227616400-227618400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:227616400-227618400	Enhancers	Right Atrium	heart
27	chr1:227616400-227618600	Enhancers	Left Ventricle	heart
28	chr1:227616400-227618600	Enhancers	NH-A	brain
29	chr1:227616400-227618800	Enhancers	Placenta	Placenta
30	chr1:227616400-227620000	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr1:227616400-227621000	Enhancers	Lung	lung
32	chr1:227616600-227619400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:227616600-227619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:227616600-227625200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:227616800-227617800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:227616800-227619400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr1:227616800-227619400	Weak transcription	Hela-S3	cervix
38	chr1:227617000-227617800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:227617000-227617800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:227617000-227617800	Flanking Active TSS	NHDF-Ad	bronchial
41	chr1:227617200-227617800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:227617200-227617800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:227617200-227617800	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr1:227617200-227617800	Enhancers	Psoas Muscle	Psoas
45	chr1:227617200-227618000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
46	chr1:227617200-227618000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:227617200-227618000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:227617200-227618000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:227617200-227618200	Flanking Active TSS	K562	blood
50	chr1:227617200-227619400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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