Variant report

Variant	rs2298019
Chromosome Location	chr1:161736035-161736036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:528)
CpG islands
(count:122)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:528 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr1:161735863-161736483	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:161735840-161736436	NB4	blood:	n/a	n/a
3	GABPA	chr1:161735769-161736582	A549	lung:	n/a	n/a
4	MXI1	chr1:161735676-161736553	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr1:161735982-161736534	K562	blood:	n/a	n/a
6	STAT3	chr1:161735779-161736764	GM12878	blood:	n/a	chr1:161736288-161736296
7	GATA3	chr1:161735670-161736696	A549	lung:	n/a	n/a
8	YY1	chr1:161735907-161736291	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr1:161735967-161736420	MCF-7	breast:	n/a	n/a
10	CEBPD	chr1:161735838-161736316	K562	blood:	n/a	n/a
11	CEBPB	chr1:161735715-161736683	GM12878	blood:	n/a	n/a
12	ARID3A	chr1:161734867-161736503	HepG2	liver:	n/a	n/a
13	ETS1	chr1:161735738-161736403	A549	lung:	n/a	chr1:161736340-161736353
14	HDAC2	chr1:161735895-161736550	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr1:161735891-161736397	GM12878	blood:	n/a	n/a
16	GATA3	chr1:161735956-161736324	MCF-7	breast:	n/a	n/a
17	MXI1	chr1:161734401-161736955	SK-N-SH	brain:	n/a	n/a
18	REST	chr1:161735937-161736217	Hela-S3	cervix:	n/a	n/a
19	ZEB1	chr1:161736009-161736126	GM12878	blood:	n/a	n/a
20	ELF1	chr1:161735708-161736659	MCF-7	breast:	n/a	n/a
21	EP300	chr1:161735678-161736442	A549	lung:	n/a	chr1:161736096-161736105
22	TBP	chr1:161735857-161736289	HepG2	liver:	n/a	n/a
23	ZEB1	chr1:161735969-161736218	GM12878	blood:	n/a	n/a
24	YY1	chr1:161735819-161736343	SK-N-SH_RA	brain:	n/a	n/a
25	POLR2A	chr1:161735733-161736400	HUVEC	blood vessel:	n/a	n/a
26	FOXA2	chr1:161735656-161736460	A549	lung:	n/a	n/a
27	GATA1	chr1:161735757-161736568	PBDE	blood:	n/a	n/a
28	USF2	chr1:161735862-161736857	Hela-S3	cervix:	n/a	n/a
29	RELA	chr1:161735767-161736553	GM18951	blood:	n/a	n/a
30	TAF1	chr1:161735838-161736269	SK-N-SH	brain:	n/a	n/a
31	TBP	chr1:161735922-161736275	H1-hESC	embryonic stem cell:	n/a	n/a
32	GATA3	chr1:161735785-161736447	SK-N-SH	brain:	n/a	n/a
33	SIN3AK20	chr1:161735815-161736367	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:161735769-161736296	HepG2	liver:	n/a	n/a
35	SPI1	chr1:161735866-161736748	HL-60	blood:	n/a	n/a
36	HNF4G	chr1:161735855-161736224	HepG2	liver:	n/a	n/a
37	HDAC2	chr1:161735956-161736243	K562	blood:	n/a	n/a
38	POLR2A	chr1:161735879-161736291	HUVEC	blood vessel:	n/a	n/a
39	STAT5A	chr1:161735807-161736462	K562	blood:	n/a	chr1:161736288-161736296
40	POLR2A	chr1:161735958-161736659	HL-60	blood:	n/a	n/a
41	TAF1	chr1:161735950-161736335	GM12891	blood:	n/a	n/a
42	MTA3	chr1:161735688-161736773	GM12878	blood:	n/a	n/a
43	ZBTB33	chr1:161735778-161736406	A549	lung:	n/a	n/a
44	ELF1	chr1:161735804-161736385	A549	lung:	n/a	n/a
45	MAX	chr1:161735854-161736365	MCF-7	breast:	n/a	n/a
46	POLR2A	chr1:161735989-161736407	A549	lung:	n/a	n/a
47	NFIC	chr1:161735695-161736482	GM12878	blood:	n/a	n/a
48	EP300	chr1:161735835-161736256	SK-N-SH_RA	brain:	n/a	chr1:161736096-161736105
49	GATA3	chr1:161735822-161736333	A549	lung:	n/a	n/a
50	PAX5	chr1:161735878-161736254	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:161736000-161736050	GM06990	blood:	n/a
2	chr1:161736000-161736050	PFSK-1	brain:	n/a
3	chr1:161736013-161736063	HMEC	breast:	n/a
4	chr1:161736000-161736050	HPAEpiC	pulmonary alveolar:	n/a
5	chr1:161736013-161736063	Hepatocyte	liver:	n/a
6	chr1:161736013-161736063	GM06990	blood:	n/a
7	chr1:161736000-161736050	AG09319	gingival:	n/a
8	chr1:161736013-161736063	SAEC	small airway:	n/a
9	chr1:161736013-161736063	HL-60	blood:	n/a
10	chr1:161736013-161736063	AG04449	skin:	fetal
11	chr1:161736013-161736063	GM12892	blood:	n/a
12	chr1:161736000-161736050	NT2-D1	testis:	n/a
13	chr1:161736000-161736050	GM12892	blood:	n/a
14	chr1:161736000-161736050	GM12878	blood:	n/a
15	chr1:161736000-161736050	HIPEpiC	eye:	n/a
16	chr1:161736013-161736063	NB4	blood:	n/a
17	chr1:161736013-161736063	HRE	kidney:	n/a
18	chr1:161736000-161736050	NHBE	bronchial:	n/a
19	chr1:161736013-161736063	HUVEC	blood vessel:	n/a
20	chr1:161736013-161736063	ProgFib	skin:	n/a
21	chr1:161736013-161736063	MCF10A-Er-Src	breast:	n/a
22	chr1:161736000-161736050	SK-N-SH	brain:	n/a
23	chr1:161736013-161736063	Caco-2	colon:	n/a
24	chr1:161736000-161736050	A549	lung:	n/a
25	chr1:161736013-161736063	HAEpiC	amniotic membrane:	n/a
26	chr1:161736000-161736050	BE2_C	brain:	n/a
27	chr1:161736013-161736063	ovcar-3	ovarian:	n/a
28	chr1:161736000-161736050	AG04449	skin:	fetal
29	chr1:161736000-161736050	AG10803	skin:	n/a
30	chr1:161736000-161736050	PrEC	prostate:	n/a
31	chr1:161736000-161736050	HCT-116	colon:	n/a
32	chr1:161736013-161736063	H1-hESC	embryonic stem cell:	embryo
33	chr1:161736000-161736050	MCF-7	breast:	n/a
34	chr1:161736013-161736063	AG10803	skin:	n/a
35	chr1:161736000-161736050	U87	brain:	n/a
36	chr1:161736000-161736050	HRPEpiC	eye:	n/a
37	chr1:161736013-161736063	GM19239	blood:	n/a
38	chr1:161736013-161736063	SK-N-SH	brain:	n/a
39	chr1:161736000-161736050	IMR90	lung:	fetal
40	chr1:161736013-161736063	HCPEpiC	choroid plexus:	n/a
41	chr1:161736000-161736050	BJ	skin:	n/a
42	chr1:161736013-161736063	NT2-D1	testis:	n/a
43	chr1:161736013-161736063	HEK293	kidney:	embryo
44	chr1:161736000-161736050	SAEC	small airway:	n/a
45	chr1:161736000-161736050	HCF	heart:	n/a
46	chr1:161736000-161736050	AG09309	skin:	n/a
47	chr1:161736000-161736050	HL-60	blood:	n/a
48	chr1:161736000-161736050	T-47D	breast:	n/a
49	chr1:161736000-161736050	HEK293	kidney:	embryo
50	chr1:161736000-161736050	NB4	blood:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
2	chr1:161015575..161016271-chr1:161735870..161736519,2	Hela-S3	cervix:
3	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
4	chr1:161735452..161736318-chr6:111136746..111137492,2	Hela-S3	cervix:
5	chr1:161735670..161736507-chr11:68671028..68671653,2	Hela-S3	cervix:
6	chr1:161735480..161736094-chr5:43556295..43557137,2	Hela-S3	cervix:
7	chr1:161718427..161720383-chr1:161735445..161737521,2	MCF-7	breast:
8	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:

No data

Variant related genes	Relation type
ATF6	TF binding region
ENSG00000226889	TF binding region
ENSG00000226889	CpG island
ATF6	CpG island
ENSG00000132740	Chromatin interaction
ENSG00000155111	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000172239	Chromatin interaction
ENSG00000197345	Chromatin interaction
ENSG00000081721	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10733044	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10737502	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753645	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753666	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10800068	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1394070	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553444	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1806594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2055539	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2134690	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134696	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2341468	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2341479	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2499856	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2880055	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34312480	0.90[ASN][1000 genomes]
rs34461550	1.00[ASN][1000 genomes]
rs35621393	0.97[ASN][1000 genomes]
rs36080602	0.90[ASN][1000 genomes]
rs3767633	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233380	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4300199	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4579731	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656335	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656339	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4657103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427633	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6427639	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6667896	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6685369	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698065	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6701754	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs71639910	0.89[ASN][1000 genomes]
rs7517386	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7532448	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924777	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2298019	ENSG00000118217	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161733600-161737000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:161733800-161737400	Active TSS	A549	lung
3	chr1:161734600-161736200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:161734600-161736400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161734600-161736400	Active TSS	Adipose Nuclei	Adipose
6	chr1:161734600-161736400	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr1:161734600-161736400	Active TSS	Hela-S3	cervix
8	chr1:161734600-161736600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
9	chr1:161734600-161736600	Active TSS	Placenta	Placenta
10	chr1:161734600-161736600	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:161734600-161736600	Active TSS	Right Atrium	heart
12	chr1:161734600-161736600	Active TSS	NH-A	brain
13	chr1:161734600-161736800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:161734600-161736800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:161734600-161736800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:161734600-161736800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:161734600-161736800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:161734600-161736800	Active TSS	Fetal Intestine Large	intestine
19	chr1:161734600-161736800	Active TSS	Fetal Kidney	kidney
20	chr1:161734600-161736800	Active TSS	Fetal Muscle Leg	muscle
21	chr1:161734600-161736800	Active TSS	Fetal Stomach	stomach
22	chr1:161734600-161736800	Active TSS	HSMM	muscle
23	chr1:161734600-161736800	Active TSS	HSMMtube	muscle
24	chr1:161734600-161736800	Active TSS	HUVEC	blood vessel
25	chr1:161734600-161736800	Active TSS	NHDF-Ad	bronchial
26	chr1:161734600-161736800	Active TSS	NHEK	skin
27	chr1:161734600-161737000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr1:161734600-161737000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr1:161734600-161737000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr1:161734600-161737000	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr1:161734600-161737000	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr1:161734600-161737000	Active TSS	Muscle Satellite Cultured Cells	--
33	chr1:161734600-161737000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:161734600-161737000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr1:161734600-161737000	Active TSS	Aorta	Aorta
36	chr1:161734600-161737000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:161734600-161737000	Active TSS	Ovary	ovary
38	chr1:161734600-161737000	Active TSS	Stomach Smooth Muscle	stomach
39	chr1:161734600-161737000	Active TSS	GM12878-XiMat	blood
40	chr1:161734600-161737000	Active TSS	NHLF	lung
41	chr1:161734600-161737200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:161734600-161737200	Active TSS	Right Ventricle	heart
43	chr1:161734600-161737400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr1:161734600-161737600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:161734800-161736400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:161734800-161736400	Active TSS	Duodenum Mucosa	Duodenum
47	chr1:161734800-161736400	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr1:161734800-161736400	Active TSS	Thymus	Thymus
49	chr1:161734800-161736600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:161734800-161736600	Active TSS	Cortex derived primary cultured neurospheres	brain

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