Variant report

Variant	rs1979638
Chromosome Location	chr1:151990981-151990982
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:151990880-151991030	HEK293	kidney:	n/a	n/a
2	CTCF	chr1:151990860-151991010	AG04449	skin:	n/a	n/a
3	CTCF	chr1:151990860-151991010	HMF	breast:	n/a	n/a
4	CTCF	chr1:151990860-151991010	NB4	blood:	n/a	n/a
5	CTCF	chr1:151990860-151991010	HFF-Myc	foreskin:	n/a	n/a
6	CTCF	chr1:151990880-151991030	K562	blood:	n/a	n/a
7	FOXA2	chr1:151990976-151991454	A549	lung:	n/a	n/a
8	CTCF	chr1:151990895-151991416	A549	lung:	n/a	n/a
9	CTCF	chr1:151990841-151991533	A549	lung:	n/a	n/a
10	CTCF	chr1:151990934-151991482	HCT-116	colon:	n/a	n/a
11	CTCF	chr1:151990930-151991476	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr1:151990860-151991010	AG04450	lung:	n/a	n/a
13	CTCF	chr1:151990920-151991070	NHLF	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151880725..151882299-chr1:151990398..151992995,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OAZ3-3	chr1:151989376-151991004	ENSG00000229021.2
2	lnc-OAZ3-3	chr1:151990754-151991004	NONHSAT139905

No data

Variant related genes	Relation type
ENSG00000240667	TF binding region
ENSG00000159445	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11204923	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387834	0.84[ASN][1000 genomes]
rs1387835	0.81[ASN][1000 genomes]
rs1473493	0.84[ASN][1000 genomes]
rs1473495	0.84[ASN][1000 genomes]
rs1490188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1490191	0.87[CEU][hapmap]
rs1532132	0.84[ASN][1000 genomes]
rs1552607	0.84[ASN][1000 genomes]
rs1602252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1602254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1873311	0.88[CEU][hapmap];0.84[ASN][1000 genomes]
rs1967084	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967085	0.87[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2338018	0.84[ASN][1000 genomes]
rs2932567	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932572	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2932588	0.84[ASN][1000 genomes]
rs2932591	0.84[ASN][1000 genomes]
rs2932592	0.84[ASN][1000 genomes]
rs2932595	0.84[ASN][1000 genomes]
rs2932596	0.84[ASN][1000 genomes]
rs2932597	0.84[ASN][1000 genomes]
rs2999514	0.87[CEU][hapmap];0.84[ASN][1000 genomes]
rs2999515	0.84[ASN][1000 genomes]
rs2999518	0.84[ASN][1000 genomes]
rs2999520	0.84[ASN][1000 genomes]
rs2999522	0.84[ASN][1000 genomes]
rs2999524	0.84[ASN][1000 genomes]
rs2999525	0.84[ASN][1000 genomes]
rs2999527	0.88[CEU][hapmap];0.84[ASN][1000 genomes]
rs2999529	0.84[ASN][1000 genomes]
rs2999535	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999536	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2999537	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999538	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2999558	1.00[ASN][1000 genomes]
rs3007701	0.84[ASN][1000 genomes]
rs3007713	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587641	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704157	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882099	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs882100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs959945	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs994974	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
5	nsv946389	chr1:151987731-151995842	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151976800-151993600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:151986600-151996200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:151986800-152007400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:151988600-151992400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:151988600-152002600	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:151988600-152004000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:151989800-151994000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:151989800-151994000	Weak transcription	HMEC	breast
9	chr1:151989800-151994400	Weak transcription	NHEK	skin
10	chr1:151989800-151994800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:151990000-151993200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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