Variant report

Variant	rs13107892
Chromosome Location	chr4:99852395-99852396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr4:99851668-99852467	HEK293	kidney:	n/a	n/a
2	ZNF143	chr4:99852225-99852456	H1-hESC	embryonic stem cell:	n/a	n/a
3	SETDB1	chr4:99850509-99852492	U2OS	brain:	n/a	chr4:99850662-99850686
4	CBX3	chr4:99852142-99852507	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:99852387-99852437	SAEC	small airway:	n/a
2	chr4:99852387-99852437	SKMC	muscle:	n/a
3	chr4:99852387-99852437	PANC-1	pancreas:	n/a
4	chr4:99852387-99852437	LNCaP	prostate:	n/a
5	chr4:99852387-99852437	K562	blood:	n/a
6	chr4:99852387-99852437	SK-N-SH_RA	brain:	n/a
7	chr4:99852387-99852437	AG09309	skin:	n/a
8	chr4:99852387-99852437	T-47D	breast:	n/a
9	chr4:99852387-99852437	H1-hESC	embryonic stem cell:	embryo
10	chr4:99852387-99852437	Hepatocyte	liver:	n/a
11	chr4:99852387-99852437	AoSMC	blood vessel:	n/a
12	chr4:99852387-99852437	RPTEC	kidney:	n/a
13	chr4:99852387-99852437	IMR90	lung:	fetal
14	chr4:99852387-99852437	GM12878	blood:	n/a
15	chr4:99852387-99852437	AG04449	skin:	fetal
16	chr4:99852387-99852437	HUVEC	blood vessel:	n/a
17	chr4:99852387-99852437	MCF-7	breast:	n/a
18	chr4:99852387-99852437	HEEpiC	esophagus:	n/a
19	chr4:99852387-99852437	HCPEpiC	choroid plexus:	n/a
20	chr4:99852387-99852437	BJ	skin:	n/a
21	chr4:99852387-99852437	AG10803	skin:	n/a
22	chr4:99852387-99852437	HRPEpiC	eye:	n/a
23	chr4:99852387-99852437	HRE	kidney:	n/a
24	chr4:99852387-99852437	GM06990	blood:	n/a
25	chr4:99852387-99852437	Hela-S3	cervix:	n/a
26	chr4:99852387-99852437	GM19239	blood:	n/a
27	chr4:99852387-99852437	A549	lung:	n/a
28	chr4:99852387-99852437	U87	brain:	n/a
29	chr4:99852387-99852437	SK-N-MC	brain:	n/a
30	chr4:99852387-99852437	PrEC	prostate:	n/a
31	chr4:99852387-99852437	CMK	blood:	n/a
32	chr4:99852387-99852437	GM12892	blood:	n/a
33	chr4:99852387-99852437	HMEC	breast:	n/a
34	chr4:99852387-99852437	HNPCEpiC	eye:	n/a
35	chr4:99852387-99852437	AG09319	gingival:	n/a
36	chr4:99852387-99852437	BE2_C	brain:	n/a
37	chr4:99852387-99852437	HIPEpiC	eye:	n/a
38	chr4:99852387-99852437	Jurkat	blood:	n/a
39	chr4:99852387-99852437	PFSK-1	brain:	n/a
40	chr4:99852387-99852437	HPAEpiC	pulmonary alveolar:	n/a
41	chr4:99852387-99852437	GM12891	blood:	n/a
42	chr4:99852387-99852437	HAEpiC	amniotic membrane:	n/a
43	chr4:99852387-99852437	NT2-D1	testis:	n/a
44	chr4:99852387-99852437	ovcar-3	ovarian:	n/a
45	chr4:99852387-99852437	Caco-2	colon:	n/a
46	chr4:99852387-99852437	MCF10A-Er-Src	breast:	n/a
47	chr4:99852387-99852437	SK-N-SH	brain:	n/a
48	chr4:99852387-99852437	HRCEpiC	kidney:	n/a
49	chr4:99852387-99852437	ECC-1	luminal epithelium:	n/a
50	chr4:99852387-99852437	HCT-116	colon:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:99849107..99853067-chr4:99958393..99961916,5	K562	blood:
2	chr4:99849574..99853806-chr4:100008192..100011466,4	MCF-7	breast:
3	chr4:99846410..99852563-chr4:99914756..99918771,11	MCF-7	breast:
4	chr4:99842136..99852937-chr4:99913200..99922220,39	K562	blood:
5	chr4:99850538..99853067-chr4:99958598..99961528,2	K562	blood:
6	chr4:99844460..99852883-chr4:99909835..99921707,41	K562	blood:
7	chr4:99848578..99852948-chr4:99876464..99882582,7	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-METAP1-4	chr4:99852298-99852458	NONHSAT097505

No data

Variant related genes	Relation type
EIF4E	TF binding region
ENSG00000238449	TF binding region
EIF4E	CpG island
ENSG00000238449	CpG island
ENSG00000197894	Chromatin interaction
ENSG00000265213	Chromatin interaction
ENSG00000214886	Chromatin interaction
ENSG00000164024	Chromatin interaction
ENSG00000246090	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1154412	1.00[ASN][1000 genomes]
rs11722494	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727079	0.81[CEU][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.96[MKK][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11727086	0.87[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731092	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11735758	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736580	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13107184	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13110878	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115072	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115688	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13124855	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13127259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130454	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133934	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13832	1.00[ASN][1000 genomes]
rs17511498	0.87[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17570252	0.87[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17583053	0.87[CEU][hapmap];0.92[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992569	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2004994	1.00[ASN][1000 genomes]
rs2230574	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3018048	1.00[ASN][1000 genomes]
rs34116542	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34164768	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34445885	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34552530	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34849916	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35019647	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35360485	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35619083	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35885444	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36061550	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699369	0.87[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699689	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699692	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323189	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323190	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62323206	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67650226	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692635	1.00[ASN][1000 genomes]
rs7688221	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688461	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896992	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv879654	chr4:99748988-99877402	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99851400-99853000	Enhancers	Primary B cells from peripheral blood	blood
2	chr4:99851400-99858000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr4:99851600-99852400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr4:99851800-99852400	Enhancers	Monocytes-CD14+_RO01746	blood
5	chr4:99851800-99853600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:99851800-99853800	Weak transcription	HSMM	muscle
7	chr4:99851800-99853800	Weak transcription	HSMMtube	muscle
8	chr4:99852000-99852400	Enhancers	K562	blood
9	chr4:99852000-99853400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:99852000-99853600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:99852000-99853600	Weak transcription	Primary B cells from cord blood	blood
12	chr4:99852000-99853600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:99852000-99853600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr4:99852000-99853600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:99852000-99853600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:99852000-99853600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr4:99852000-99853600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr4:99852000-99853600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:99852000-99853600	Weak transcription	GM12878-XiMat	blood
20	chr4:99852000-99853600	Weak transcription	NHEK	skin
21	chr4:99852000-99853600	Weak transcription	Osteobl	bone
22	chr4:99852000-99853800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:99852000-99853800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:99852000-99853800	Weak transcription	NHDF-Ad	bronchial
25	chr4:99852000-99854000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr4:99852000-99854000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:99852000-99854200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr4:99852000-99855800	Weak transcription	HepG2	liver
29	chr4:99852000-99859000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr4:99852000-99859000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:99852000-99859200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr4:99852000-99859400	Weak transcription	Stomach Mucosa	stomach
33	chr4:99852200-99852600	Weak transcription	HUVEC	blood vessel
34	chr4:99852200-99859400	Weak transcription	HMEC	breast

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