Variant report

Variant	rs1398028
Chromosome Location	chr2:111966222-111966223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr2:111965967-111967091	GM12878	blood:	n/a	chr2:111966567-111966578
2	WRNIP1	chr2:111965966-111967108	GM12878	blood:	n/a	n/a
3	RFX5	chr2:111966217-111966286	GM12878	blood:	n/a	n/a
4	MAX	chr2:111966195-111967149	GM12878	blood:	n/a	n/a
5	USF2	chr2:111966108-111966317	GM12878	blood:	n/a	n/a
6	RELA	chr2:111966191-111967124	GM12878	blood:	n/a	n/a
7	RELA	chr2:111965881-111967171	GM18951	blood:	n/a	n/a
8	TBL1XR1	chr2:111966154-111967178	GM12878	blood:	n/a	n/a
9	RCOR1	chr2:111966193-111967181	GM12878	blood:	n/a	n/a
10	ELK1	chr2:111966173-111966345	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111876826..111879311-chr2:111966028..111968773,2	K562	blood:
2	chr2:111963419..111965229-chr2:111965718..111968351,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC108463.1-3	chr2:111964138-111966238	NONHSAT073620
2	lnc-AC108463.1-3	chr2:111965359-111966238	NONHSAT073622
3	lnc-AC108463.1-3	chr2:111965991-111966616	NONHSAT073625
4	lnc-BCL2L11-6	chr2:111965578-111966309	ucscGeneNc_uc002thg_1
5	lnc-AC108463.1-3	chr2:111965353-111966238	ENSG00000172965.6
6	lnc-AC108463.1-3	chr2:111965592-111966694	ENSG00000172965.10

No data

Variant related genes	Relation type
ENSG00000227992	TF binding region
ENSG00000227992	Chromatin interaction
ENSG00000153094	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12989258	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464023	0.85[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1949138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2055924	0.84[ASN][1000 genomes]
rs62160379	0.81[ASN][1000 genomes]
rs6713056	1.00[ASW][hapmap]
rs6719531	1.00[ASW][hapmap]
rs6747781	0.98[ASN][1000 genomes]
rs938096	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	esv1803356	chr2:111899783-112662597	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv428402	chr2:111899783-112662597	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1801950	chr2:111899783-112746937	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	esv2757825	chr2:111899783-112746937	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv2759083	chr2:111899783-112746937	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111950200-111969600	Weak transcription	Dnd41	blood
2	chr2:111952200-111974800	Weak transcription	Aorta	Aorta
3	chr2:111953000-111968000	Weak transcription	K562	blood
4	chr2:111954800-112006800	Weak transcription	HUVEC	blood vessel
5	chr2:111957200-111972400	Weak transcription	NHLF	lung
6	chr2:111958000-111974400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:111958400-111967600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:111958400-111968600	Weak transcription	HepG2	liver
9	chr2:111958400-111972000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:111958400-111974200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:111960600-111966400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:111962600-111974400	Weak transcription	Left Ventricle	heart
13	chr2:111963400-111966400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:111964600-111966600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:111964800-111967800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:111965000-111966400	Enhancers	Fetal Intestine Large	intestine
17	chr2:111965200-111966400	Enhancers	Fetal Intestine Small	intestine
18	chr2:111965400-111966400	Strong transcription	NHDF-Ad	bronchial
19	chr2:111965600-111966400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr2:111965600-111966400	Enhancers	GM12878-XiMat	blood
21	chr2:111965600-111967600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:111965800-111966400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:111966000-111966600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:111966000-111967200	Enhancers	Primary B cells from peripheral blood	blood
25	chr2:111966200-111966400	Genic enhancers	HSMM	muscle
26	chr2:111966200-111966600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:111966200-111966600	Weak transcription	HSMMtube	muscle
28	chr2:111966200-111967000	Enhancers	Osteobl	bone
29	chr2:111966200-111967200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr2:111966200-111967200	Enhancers	NH-A	brain
31	chr2:111966200-111969400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:111966200-111971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:111966200-111974400	Weak transcription	Lung	lung

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