Variant report

Variant	rs1360465
Chromosome Location	chr9:2571403-2571404
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr9:2570558-2571524	HEK293	kidney:	n/a	n/a
2	TFAP2C	chr9:2570622-2571453	Hela-S3	cervix:	n/a	n/a
3	STAT1	chr9:2570531-2571412	Hela-S3	cervix:	n/a	chr9:2571015-2571022 chr9:2570777-2570786
4	SP1	chr9:2570573-2571446	A549	lung:	n/a	n/a
5	ZKSCAN1	chr9:2570615-2571412	Hela-S3	cervix:	n/a	n/a
6	BRCA1	chr9:2570638-2571415	Hela-S3	cervix:	n/a	n/a
7	KAP1	chr9:2570608-2571513	U2OS	brain:	n/a	n/a
8	FOS	chr9:2570598-2571415	HUVEC	blood vessel:	n/a	chr9:2570776-2570786 chr9:2570777-2570786 chr9:2571006-2571018 chr9:2570776-2570786 chr9:2570776-2570786

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr9:2571396-2571446	SKMC	muscle:	n/a
2	chr9:2571396-2571446	AG04449	skin:	fetal
3	chr9:2571396-2571446	MCF-7	breast:	n/a
4	chr9:2571396-2571446	HepG2	liver:	n/a
5	chr9:2571396-2571446	PrEC	prostate:	n/a
6	chr9:2571396-2571446	U87	brain:	n/a
7	chr9:2571396-2571446	PANC-1	pancreas:	n/a
8	chr9:2571396-2571446	GM12878	blood:	n/a
9	chr9:2571396-2571446	ovcar-3	ovarian:	n/a
10	chr9:2571396-2571446	HIPEpiC	eye:	n/a
11	chr9:2571396-2571446	A549	lung:	n/a
12	chr9:2571396-2571446	NHBE	bronchial:	n/a
13	chr9:2571396-2571446	HCF	heart:	n/a
14	chr9:2571396-2571446	Jurkat	blood:	n/a
15	chr9:2571396-2571446	HEEpiC	esophagus:	n/a
16	chr9:2571396-2571446	HL-60	blood:	n/a
17	chr9:2571396-2571446	BJ	skin:	n/a
18	chr9:2571396-2571446	GM12891	blood:	n/a
19	chr9:2571396-2571446	HRCEpiC	kidney:	n/a
20	chr9:2571396-2571446	Hepatocyte	liver:	n/a
21	chr9:2571396-2571446	NHDF-neo	bronchial:	n/a
22	chr9:2571396-2571446	HCT-116	colon:	n/a
23	chr9:2571396-2571446	Hela-S3	cervix:	n/a
24	chr9:2571396-2571446	Caco-2	colon:	n/a
25	chr9:2571396-2571446	MCF10A-Er-Src	breast:	n/a
26	chr9:2571396-2571446	AG09309	skin:	n/a
27	chr9:2571396-2571446	GM12892	blood:	n/a
28	chr9:2571396-2571446	BE2_C	brain:	n/a
29	chr9:2571396-2571446	SK-N-SH_RA	brain:	n/a
30	chr9:2571396-2571446	IMR90	lung:	fetal
31	chr9:2571396-2571446	HAEpiC	amniotic membrane:	n/a
32	chr9:2571396-2571446	H1-hESC	embryonic stem cell:	embryo
33	chr9:2571396-2571446	AG09319	gingival:	n/a
34	chr9:2571396-2571446	HEK293	kidney:	embryo
35	chr9:2571396-2571446	LNCaP	prostate:	n/a
36	chr9:2571396-2571446	AoSMC	blood vessel:	n/a
37	chr9:2571396-2571446	HNPCEpiC	eye:	n/a
38	chr9:2571396-2571446	T-47D	breast:	n/a
39	chr9:2571396-2571446	AG10803	skin:	n/a
40	chr9:2571396-2571446	NH-A	brain:	n/a
41	chr9:2571396-2571446	HRPEpiC	eye:	n/a
42	chr9:2571396-2571446	GM19239	blood:	n/a
43	chr9:2571396-2571446	HPAEpiC	pulmonary alveolar:	n/a
44	chr9:2571396-2571446	SAEC	small airway:	n/a
45	chr9:2571396-2571446	GM06990	blood:	n/a
46	chr9:2571396-2571446	ProgFib	skin:	n/a
47	chr9:2571396-2571446	K562	blood:	n/a
48	chr9:2571396-2571446	NB4	blood:	n/a
49	chr9:2571396-2571446	HCM	heart:	n/a
50	chr9:2571396-2571446	RPTEC	kidney:	n/a

No data

Variant related genes	Relation type
ENSG00000236404	TF binding region
ENSG00000236404	CpG island

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10812242	0.86[CHB][hapmap]
rs10966879	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10967016	0.91[CEU][hapmap];0.86[CHB][hapmap];0.85[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10967148	0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs12336420	0.87[ASN][1000 genomes]
rs12337311	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12337543	0.83[ASN][1000 genomes]
rs12340260	0.85[ASN][1000 genomes]
rs12350335	0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs12350342	0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs12378034	0.87[ASN][1000 genomes]
rs12378113	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs1590979	0.86[CHB][hapmap]
rs16907400	1.00[JPT][hapmap]
rs1707299	0.86[CHB][hapmap]
rs1707300	0.86[CHB][hapmap]
rs17488507	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2492589	0.86[CHB][hapmap]
rs494035	0.86[CHB][hapmap]
rs521856	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538311	0.86[CHB][hapmap]
rs541062	0.86[CHB][hapmap]
rs542616	0.86[CHB][hapmap]
rs542859	0.86[CHB][hapmap];1.00[CHD][hapmap]
rs544832	0.86[CHB][hapmap]
rs55755264	0.83[ASN][1000 genomes]
rs55998465	0.87[ASN][1000 genomes]
rs581859	0.86[CHB][hapmap]
rs596826	0.86[CHB][hapmap]
rs67779684	0.87[ASN][1000 genomes]
rs693934	0.86[CHB][hapmap]
rs7873747	0.83[ASN][1000 genomes]
rs882259	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
11	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
13	nsv1033424	chr9:2508296-2575408	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1029876	chr9:2526760-2633562	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv892068	chr9:2543888-2589739	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 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	chr9:2559800-2577000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr9:2566400-2571800	Enhancers	Adipose Nuclei	Adipose
3	chr9:2567000-2571800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:2567600-2577600	Enhancers	Fetal Heart	heart
5	chr9:2568600-2576000	Enhancers	Ovary	ovary
6	chr9:2569000-2572400	Weak transcription	Left Ventricle	heart
7	chr9:2569000-2575400	Weak transcription	Right Ventricle	heart
8	chr9:2569600-2571600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:2570000-2572000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr9:2570600-2571600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:2570600-2571600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:2570600-2571600	Enhancers	Muscle Satellite Cultured Cells	--
13	chr9:2570600-2571600	Enhancers	Liver	Liver
14	chr9:2570600-2571600	Enhancers	Colon Smooth Muscle	Colon
15	chr9:2570600-2571600	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr9:2570600-2571600	Enhancers	Fetal Intestine Small	intestine
17	chr9:2570600-2571600	Enhancers	NHEK	skin
18	chr9:2570600-2571600	Enhancers	Osteobl	bone
19	chr9:2570600-2571800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:2570600-2571800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:2570600-2571800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:2570600-2571800	Enhancers	Fetal Muscle Leg	muscle
23	chr9:2570600-2571800	Enhancers	Placenta	Placenta
24	chr9:2570600-2571800	Enhancers	HMEC	breast
25	chr9:2570600-2572000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr9:2570600-2572000	Enhancers	Stomach Mucosa	stomach
27	chr9:2570600-2572000	Enhancers	Hela-S3	cervix
28	chr9:2570800-2571600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr9:2570800-2571600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:2570800-2571600	Enhancers	Fetal Kidney	kidney
31	chr9:2570800-2571600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr9:2570800-2571800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:2570800-2572000	Enhancers	Fetal Lung	lung
34	chr9:2571000-2571800	Enhancers	HSMM	muscle
35	chr9:2571000-2572000	Enhancers	HSMMtube	muscle
36	chr9:2571000-2573200	Enhancers	Right Atrium	heart
37	chr9:2571000-2574200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:2571200-2571600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:2571200-2571600	Enhancers	Fetal Intestine Large	intestine
40	chr9:2571200-2571600	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr9:2571200-2571600	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr9:2571200-2571600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr9:2571200-2573200	Enhancers	Psoas Muscle	Psoas
44	chr9:2571400-2571600	Flanking Active TSS	A549	lung
45	chr9:2571400-2571800	Enhancers	Rectal Mucosa Donor 29	rectum
46	chr9:2571400-2573200	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr9:2571400-2574000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr9:2571400-2574200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:2571400-2574400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:2571400-2576600	Weak transcription	Brain Substantia Nigra	brain

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