Variant report

Variant	rs809601
Chromosome Location	chr10:44789602-44789603
allele	A/G
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:0)
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	CEBPB	chr10:44789236-44789628	IMR90	lung:	n/a	n/a
2	POLR2A	chr10:44789239-44789708	U87	brain:	n/a	n/a
3	POLR2A	chr10:44788687-44789713	U87	brain:	n/a	n/a
4	POLR2A	chr10:44789249-44789681	U87	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:44789589-44789639	HCF	heart:	n/a
2	chr10:44789589-44789639	ECC-1	luminal epithelium:	n/a
3	chr10:44789589-44789639	GM12891	blood:	n/a
4	chr10:44789589-44789639	Caco-2	colon:	n/a
5	chr10:44789589-44789639	BJ	skin:	n/a
6	chr10:44789589-44789639	AG04450	lung:	fetal
7	chr10:44789589-44789639	HEK293	kidney:	embryo
8	chr10:44789589-44789639	H1-hESC	embryonic stem cell:	embryo
9	chr10:44789589-44789639	PANC-1	pancreas:	n/a
10	chr10:44789589-44789639	GM19239	blood:	n/a
11	chr10:44789589-44789639	SKMC	muscle:	n/a
12	chr10:44789589-44789639	HMEC	breast:	n/a
13	chr10:44789589-44789639	HCM	heart:	n/a
14	chr10:44789589-44789639	HRPEpiC	eye:	n/a
15	chr10:44789589-44789639	RPTEC	kidney:	n/a
16	chr10:44789589-44789639	HL-60	blood:	n/a
17	chr10:44789589-44789639	IMR90	lung:	fetal
18	chr10:44789589-44789639	AG09309	skin:	n/a
19	chr10:44789589-44789639	CMK	blood:	n/a
20	chr10:44789589-44789639	GM12892	blood:	n/a
21	chr10:44789589-44789639	HepG2	liver:	n/a
22	chr10:44789589-44789639	NB4	blood:	n/a
23	chr10:44789589-44789639	AoSMC	blood vessel:	n/a
24	chr10:44789589-44789639	Jurkat	blood:	n/a
25	chr10:44789589-44789639	HNPCEpiC	eye:	n/a
26	chr10:44789589-44789639	U87	brain:	n/a
27	chr10:44789589-44789639	HCPEpiC	choroid plexus:	n/a
28	chr10:44789589-44789639	NT2-D1	testis:	n/a
29	chr10:44789589-44789639	LNCaP	prostate:	n/a
30	chr10:44789589-44789639	Hela-S3	cervix:	n/a
31	chr10:44789589-44789639	PrEC	prostate:	n/a
32	chr10:44789589-44789639	HPAEpiC	pulmonary alveolar:	n/a
33	chr10:44789589-44789639	GM06990	blood:	n/a
34	chr10:44789589-44789639	T-47D	breast:	n/a
35	chr10:44789589-44789639	Hepatocyte	liver:	n/a
36	chr10:44789589-44789639	K562	blood:	n/a
37	chr10:44789589-44789639	NH-A	brain:	n/a
38	chr10:44789589-44789639	NHDF-neo	bronchial:	n/a
39	chr10:44789589-44789639	HCT-116	colon:	n/a
40	chr10:44789589-44789639	SK-N-SH_RA	brain:	n/a
41	chr10:44789589-44789639	AG09319	gingival:	n/a
42	chr10:44789589-44789639	MCF10A-Er-Src	breast:	n/a
43	chr10:44789589-44789639	HIPEpiC	eye:	n/a
44	chr10:44789589-44789639	SK-N-SH	brain:	n/a
45	chr10:44789589-44789639	NHBE	bronchial:	n/a
46	chr10:44789589-44789639	AG10803	skin:	n/a
47	chr10:44789589-44789639	AG04449	skin:	fetal
48	chr10:44789589-44789639	PFSK-1	brain:	n/a
49	chr10:44789589-44789639	ProgFib	skin:	n/a
50	chr10:44789589-44789639	HRE	kidney:	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CXCL12-1	chr10:44789285-44789628	XLOC_008795

No data

Variant related genes	Relation type
ENSG00000229116	TF binding region
ENSG00000229116	CpG island

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1147883	1.00[ASN][1000 genomes]
rs17156150	1.00[ASN][1000 genomes]
rs1746051	1.00[ASN][1000 genomes]
rs1746053	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146808	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs266080	1.00[ASN][1000 genomes]
rs266082	1.00[ASN][1000 genomes]
rs266083	1.00[ASN][1000 genomes]
rs2760671	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2760672	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802478	1.00[ASN][1000 genomes]
rs2802479	1.00[ASN][1000 genomes]
rs34941677	1.00[ASN][1000 genomes]
rs35155049	1.00[ASN][1000 genomes]
rs35374150	1.00[ASN][1000 genomes]
rs549054	1.00[ASN][1000 genomes]
rs702363	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71491034	1.00[ASN][1000 genomes]
rs768676	1.00[ASN][1000 genomes]
rs7918766	1.00[ASN][1000 genomes]
rs800309	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800316	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800318	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800320	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800324	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs800327	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs808972	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]
rs810236	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs812331	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1038511	chr10:44596885-44870030	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv508579	chr10:44709770-44799256	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3422728	chr10:44788646-44792944	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3352463	chr10:44789446-44792444	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44787800-44790800	Enhancers	Fetal Heart	heart
2	chr10:44787800-44791600	Enhancers	Ovary	ovary
3	chr10:44788200-44790400	Weak transcription	Pancreas	Pancrea
4	chr10:44788200-44790600	Weak transcription	Spleen	Spleen
5	chr10:44788200-44791000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr10:44788400-44789800	Enhancers	Fetal Kidney	kidney
7	chr10:44788600-44789800	Enhancers	NHLF	lung
8	chr10:44788600-44791200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr10:44788600-44791600	Enhancers	NHDF-Ad	bronchial
10	chr10:44789000-44789800	Bivalent Enhancer	Fetal Stomach	stomach
11	chr10:44789000-44790000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:44789000-44790000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr10:44789000-44790000	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr10:44789000-44790200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr10:44789000-44791400	Enhancers	GM12878-XiMat	blood
16	chr10:44789000-44791600	Enhancers	Right Ventricle	heart
17	chr10:44789200-44789800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr10:44789200-44789800	Enhancers	Fetal Lung	lung
19	chr10:44789200-44789800	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr10:44789200-44789800	Enhancers	HepG2	liver
21	chr10:44789200-44789800	Enhancers	NH-A	brain
22	chr10:44789200-44790000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
23	chr10:44789200-44790000	Enhancers	Brain Anterior Caudate	brain
24	chr10:44789200-44790200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr10:44789200-44790200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
26	chr10:44789200-44790200	Enhancers	Colon Smooth Muscle	Colon
27	chr10:44789200-44790200	Enhancers	Right Atrium	heart
28	chr10:44789200-44790400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr10:44789200-44790400	Weak transcription	Brain Substantia Nigra	brain
30	chr10:44789200-44790400	Weak transcription	Gastric	stomach
31	chr10:44789200-44791000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr10:44789200-44791000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:44789200-44791200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr10:44789200-44791400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr10:44789200-44791400	Enhancers	Rectal Smooth Muscle	rectum
36	chr10:44789200-44796600	Weak transcription	Fetal Brain Female	brain
37	chr10:44789400-44789800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr10:44789400-44789800	Weak transcription	Left Ventricle	heart
39	chr10:44789400-44789800	Weak transcription	Lung	lung
40	chr10:44789400-44790000	Enhancers	Adipose Nuclei	Adipose
41	chr10:44789400-44790000	Bivalent Enhancer	Fetal Intestine Small	intestine
42	chr10:44789400-44791000	Weak transcription	Brain Hippocampus Middle	brain
43	chr10:44789400-44791200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:44789400-44791600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:44789600-44789800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr10:44789600-44789800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
47	chr10:44789600-44789800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr10:44789600-44789800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
49	chr10:44789600-44790000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
50	chr10:44789600-44790200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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