Variant report

Variant	rs462652
Chromosome Location	chr5:9523390-9523391
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr5:9523226-9524084	MCF-7	breast:	n/a	n/a
2	GATA3	chr5:9523120-9524120	MCF-7	breast:	n/a	n/a
3	FOSL2	chr5:9523375-9523990	MCF-7	breast:	n/a	chr5:9523702-9523712 chr5:9523684-9523692 chr5:9523701-9523713 chr5:9523702-9523712 chr5:9523683-9523694 chr5:9523704-9523711 chr5:9523684-9523691 chr5:9523685-9523696 chr5:9523703-9523712 chr5:9523702-9523711 chr5:9523684-9523692

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:9523352-9523402	LNCaP	prostate:	n/a
2	chr5:9523352-9523402	U87	brain:	n/a
3	chr5:9523352-9523402	HRE	kidney:	n/a
4	chr5:9523352-9523402	AG09319	gingival:	n/a
5	chr5:9523352-9523402	GM06990	blood:	n/a
6	chr5:9523352-9523402	ovcar-3	ovarian:	n/a
7	chr5:9523352-9523402	HMEC	breast:	n/a
8	chr5:9523352-9523402	GM12892	blood:	n/a
9	chr5:9523352-9523402	HUVEC	blood vessel:	n/a
10	chr5:9523352-9523402	RPTEC	kidney:	n/a
11	chr5:9523352-9523402	SKMC	muscle:	n/a
12	chr5:9523352-9523402	PANC-1	pancreas:	n/a
13	chr5:9523352-9523402	IMR90	lung:	fetal
14	chr5:9523352-9523402	MCF-7	breast:	n/a
15	chr5:9523352-9523402	HepG2	liver:	n/a
16	chr5:9523352-9523402	K562	blood:	n/a
17	chr5:9523352-9523402	Hepatocyte	liver:	n/a
18	chr5:9523352-9523402	PFSK-1	brain:	n/a
19	chr5:9523352-9523402	NHBE	bronchial:	n/a
20	chr5:9523352-9523402	HCM	heart:	n/a
21	chr5:9523352-9523402	NB4	blood:	n/a
22	chr5:9523352-9523402	SK-N-SH_RA	brain:	n/a
23	chr5:9523352-9523402	HNPCEpiC	eye:	n/a
24	chr5:9523352-9523402	ProgFib	skin:	n/a
25	chr5:9523352-9523402	NH-A	brain:	n/a
26	chr5:9523352-9523402	ECC-1	luminal epithelium:	n/a
27	chr5:9523352-9523402	HCT-116	colon:	n/a
28	chr5:9523352-9523402	GM19239	blood:	n/a
29	chr5:9523352-9523402	AG04450	lung:	fetal
30	chr5:9523352-9523402	BJ	skin:	n/a
31	chr5:9523352-9523402	AG09309	skin:	n/a
32	chr5:9523352-9523402	PrEC	prostate:	n/a
33	chr5:9523352-9523402	HAEpiC	amniotic membrane:	n/a
34	chr5:9523352-9523402	HIPEpiC	eye:	n/a
35	chr5:9523352-9523402	HCF	heart:	n/a
36	chr5:9523352-9523402	NHDF-neo	bronchial:	n/a
37	chr5:9523352-9523402	CMK	blood:	n/a
38	chr5:9523352-9523402	SK-N-SH	brain:	n/a
39	chr5:9523352-9523402	Jurkat	blood:	n/a
40	chr5:9523352-9523402	SK-N-MC	brain:	n/a
41	chr5:9523352-9523402	Caco-2	colon:	n/a
42	chr5:9523352-9523402	GM12891	blood:	n/a
43	chr5:9523352-9523402	HEK293	kidney:	embryo
44	chr5:9523352-9523402	HRCEpiC	kidney:	n/a
45	chr5:9523352-9523402	AG04449	skin:	fetal
46	chr5:9523352-9523402	HPAEpiC	pulmonary alveolar:	n/a
47	chr5:9523352-9523402	HL-60	blood:	n/a
48	chr5:9523352-9523402	AoSMC	blood vessel:	n/a
49	chr5:9523352-9523402	SAEC	small airway:	n/a
50	chr5:9523352-9523402	H1-hESC	embryonic stem cell:	embryo

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:9519723..9521452-chr5:9523293..9526016,2	MCF-7	breast:
2	chr5:9518291..9521025-chr5:9523342..9525651,2	K562	blood:
3	chr5:9522895..9524468-chr5:9544584..9546294,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000250001	TF binding region
ENSG00000250001	CpG island
ENSG00000112902	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs13178837	0.95[EUR][1000 genomes]
rs174863	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2458362	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268544	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268545	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268546	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268547	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs268548	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268549	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs268551	0.95[EUR][1000 genomes]
rs268552	0.94[EUR][1000 genomes]
rs371458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756733	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs375779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs377791	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382409	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398533	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406583	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420819	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435329	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs439869	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446573	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs453742	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455353	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455538	0.95[EUR][1000 genomes]
rs455757	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456058	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456400	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457203	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459659	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs459789	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs459793	0.95[EUR][1000 genomes]
rs460887	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs461321	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs461415	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs461700	0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs461907	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462057	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462185	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462473	0.95[EUR][1000 genomes]
rs463004	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463029	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464267	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464616	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464975	0.82[ASN][1000 genomes]
rs465205	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs465991	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466158	0.95[EUR][1000 genomes]
rs466667	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs466883	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630768	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription 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	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9499200-9528600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:9509000-9523400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:9513000-9532800	Weak transcription	Fetal Stomach	stomach
4	chr5:9513000-9535200	Weak transcription	Aorta	Aorta
5	chr5:9517400-9523800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:9518600-9524400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr5:9518800-9525200	Weak transcription	Small Intestine	intestine
8	chr5:9520400-9523400	Weak transcription	Osteobl	bone
9	chr5:9520400-9523600	Weak transcription	Pancreas	Pancrea
10	chr5:9520400-9532800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:9520600-9523400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:9520600-9526800	Weak transcription	Left Ventricle	heart
13	chr5:9520800-9523800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:9520800-9524400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:9521200-9523400	Weak transcription	NHDF-Ad	bronchial
16	chr5:9521200-9527000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:9522200-9523600	Weak transcription	Fetal Heart	heart
19	chr5:9522200-9524200	Weak transcription	Right Ventricle	heart
20	chr5:9522200-9528600	Weak transcription	Fetal Muscle Leg	muscle
21	chr5:9522200-9529200	Weak transcription	Fetal Muscle Trunk	muscle
22	chr5:9522400-9523400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr5:9522400-9525400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:9522400-9526600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:9522600-9529400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:9522800-9527800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:9523000-9523400	Weak transcription	Fetal Kidney	kidney
28	chr5:9523200-9523400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr5:9523200-9523400	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr5:9523200-9523600	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr5:9523200-9523600	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr5:9523200-9524000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:9523200-9524000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr5:9523200-9524000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:9523200-9524000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:9523200-9524000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:9523200-9524000	Enhancers	NH-A	brain
38	chr5:9523200-9524000	Enhancers	NHLF	lung
39	chr5:9523200-9524200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr5:9523200-9524400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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