Variant report

Variant	rs62003660
Chromosome Location	chr15:74495374-74495375
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:175)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:175 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:74495322-74495449	K562	blood:	n/a	n/a
2	MTA3	chr15:74495193-74495684	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:74495248-74495488	ECC-1	luminal epithelium:	n/a	n/a
4	RAD21	chr15:74494660-74495837	SK-N-SH_RA	brain:	n/a	chr15:74494901-74494915
5	CTCF	chr15:74495360-74495510	HA-sp	spinal cord:	n/a	n/a
6	CTCF	chr15:74495340-74495490	HEEpiC	esophagus:	n/a	n/a
7	CTCF	chr15:74495340-74495490	BJ	skin:	n/a	n/a
8	ATF2	chr15:74494985-74495663	H1-hESC	embryonic stem cell:	n/a	n/a
9	USF1	chr15:74495149-74495468	A549	lung:	n/a	n/a
10	CTCF	chr15:74495360-74495510	SK-N-SH_RA	brain:	n/a	n/a
11	CTCF	chr15:74495344-74495452	GM12892	blood:	n/a	n/a
12	CTCF	chr15:74495317-74495496	MCF-7	breast:	n/a	n/a
13	EGR1	chr15:74495135-74495525	K562	blood:	n/a	chr15:74495307-74495320 chr15:74495466-74495479 chr15:74495314-74495324 chr15:74495246-74495260 chr15:74495313-74495326 chr15:74495310-74495324 chr15:74495313-74495326 chr15:74495307-74495317 chr15:74495313-74495326 chr15:74495312-74495327 chr15:74495314-74495323 chr15:74495313-74495326 chr15:74495312-74495326
14	RAD21	chr15:74495290-74495420	K562	blood:	n/a	n/a
15	YY1	chr15:74495071-74495449	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr15:74494845-74495707	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr15:74495360-74495510	HRPEpiC	eye:	n/a	n/a
18	CTCF	chr15:74495240-74495390	A549	lung:	n/a	n/a
19	CTCF	chr15:74495340-74495490	NHEK	skin:	n/a	n/a
20	TAF7	chr15:74495003-74495544	H1-hESC	embryonic stem cell:	n/a	n/a
21	SIN3AK20	chr15:74494951-74495531	H1-hESC	embryonic stem cell:	n/a	n/a
22	USF1	chr15:74495125-74495519	SK-N-SH_RA	brain:	n/a	n/a
23	POLR2A	chr15:74495252-74495507	A549	lung:	n/a	n/a
24	TEAD4	chr15:74494944-74495649	H1-hESC	embryonic stem cell:	n/a	n/a
25	EP300	chr15:74494682-74495737	SK-N-SH_RA	brain:	n/a	n/a
26	MAX	chr15:74494663-74495875	H1-hESC	embryonic stem cell:	n/a	chr15:74495240-74495250 chr15:74495165-74495175
27	GATA3	chr15:74495223-74495972	SK-N-SH	brain:	n/a	n/a
28	GABPA	chr15:74495023-74495552	H1-hESC	embryonic stem cell:	n/a	chr15:74495377-74495386
29	CTCF	chr15:74495360-74495510	MCF-7	breast:	n/a	n/a
30	CTCF	chr15:74495331-74495494	SK-N-SH_RA	brain:	n/a	n/a
31	CHD2	chr15:74495172-74495489	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr15:74495260-74495410	K562	blood:	n/a	n/a
33	CTCF	chr15:74495335-74495495	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr15:74495320-74495470	NHEK	skin:	n/a	n/a
35	CTCF	chr15:74495360-74495510	NHDF-neo	bronchial:	n/a	n/a
36	RAD21	chr15:74495126-74495669	MCF-7	breast:	n/a	n/a
37	CTCF	chr15:74495360-74495510	HMEC	breast:	n/a	n/a
38	POLR2A	chr15:74495243-74495522	A549	lung:	n/a	n/a
39	TEAD4	chr15:74495121-74495593	H1-hESC	embryonic stem cell:	n/a	n/a
40	CTCF	chr15:74495360-74495510	BJ	skin:	n/a	n/a
41	CEBPB	chr15:74495243-74495720	A549	lung:	n/a	n/a
42	CTCF	chr15:74495280-74495430	HEK293	kidney:	n/a	n/a
43	CTCF	chr15:74495360-74495510	SAEC	small airway:	n/a	n/a
44	SMARCC1	chr15:74492611-74495990	Hela-S3	cervix:	n/a	n/a
45	EGR1	chr15:74495048-74495565	H1-hESC	embryonic stem cell:	n/a	chr15:74495307-74495320 chr15:74495466-74495479 chr15:74495314-74495324 chr15:74495246-74495260 chr15:74495313-74495326 chr15:74495310-74495324 chr15:74495313-74495326 chr15:74495307-74495317 chr15:74495313-74495326 chr15:74495312-74495327 chr15:74495314-74495323 chr15:74495313-74495326 chr15:74495312-74495326
46	RUNX3	chr15:74495021-74495605	GM12878	blood:	n/a	n/a
47	CTCF	chr15:74495340-74495490	HCPEpiC	choroid plexus:	n/a	n/a
48	CTCF	chr15:74495304-74495653	K562	blood:	n/a	n/a
49	CTCF	chr15:74495340-74495490	HEK293	kidney:	n/a	n/a
50	POLR2A	chr15:74495269-74495525	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:74495354-74495404	HNPCEpiC	eye:	n/a
2	chr15:74495354-74495404	GM12891	blood:	n/a
3	chr15:74495354-74495404	AG10803	skin:	n/a
4	chr15:74495354-74495404	H1-hESC	embryonic stem cell:	embryo
5	chr15:74495354-74495404	HUVEC	blood vessel:	n/a
6	chr15:74495354-74495404	GM19239	blood:	n/a
7	chr15:74495354-74495404	HCM	heart:	n/a
8	chr15:74495354-74495404	NT2-D1	testis:	n/a
9	chr15:74495354-74495404	SK-N-MC	brain:	n/a
10	chr15:74495354-74495404	GM12892	blood:	n/a
11	chr15:74495354-74495404	HEK293	kidney:	embryo
12	chr15:74495354-74495404	HepG2	liver:	n/a
13	chr15:74495354-74495404	SAEC	small airway:	n/a
14	chr15:74495354-74495404	K562	blood:	n/a
15	chr15:74495354-74495404	IMR90	lung:	fetal
16	chr15:74495354-74495404	AG04450	lung:	fetal
17	chr15:74495354-74495404	ProgFib	skin:	n/a
18	chr15:74495354-74495404	HAEpiC	amniotic membrane:	n/a
19	chr15:74495354-74495404	Caco-2	colon:	n/a
20	chr15:74495354-74495404	HMEC	breast:	n/a
21	chr15:74495354-74495404	AG04449	skin:	fetal
22	chr15:74495354-74495404	RPTEC	kidney:	n/a
23	chr15:74495354-74495404	AG09309	skin:	n/a
24	chr15:74495354-74495404	PANC-1	pancreas:	n/a
25	chr15:74495354-74495404	HIPEpiC	eye:	n/a
26	chr15:74495354-74495404	BJ	skin:	n/a
27	chr15:74495354-74495404	A549	lung:	n/a
28	chr15:74495354-74495404	Hepatocyte	liver:	n/a
29	chr15:74495354-74495404	NB4	blood:	n/a
30	chr15:74495354-74495404	HCF	heart:	n/a
31	chr15:74495354-74495404	NH-A	brain:	n/a
32	chr15:74495354-74495404	BE2_C	brain:	n/a
33	chr15:74495354-74495404	SK-N-SH_RA	brain:	n/a
34	chr15:74495354-74495404	HRPEpiC	eye:	n/a
35	chr15:74495354-74495404	Hela-S3	cervix:	n/a
36	chr15:74495354-74495404	ECC-1	luminal epithelium:	n/a
37	chr15:74495354-74495404	ovcar-3	ovarian:	n/a
38	chr15:74495354-74495404	SKMC	muscle:	n/a
39	chr15:74495354-74495404	LNCaP	prostate:	n/a
40	chr15:74495354-74495404	AoSMC	blood vessel:	n/a
41	chr15:74495354-74495404	AG09319	gingival:	n/a
42	chr15:74495354-74495404	CMK	blood:	n/a
43	chr15:74495354-74495404	PFSK-1	brain:	n/a
44	chr15:74495354-74495404	PrEC	prostate:	n/a
45	chr15:74495354-74495404	NHDF-neo	bronchial:	n/a
46	chr15:74495354-74495404	GM06990	blood:	n/a
47	chr15:74495354-74495404	HL-60	blood:	n/a
48	chr15:74495354-74495404	Jurkat	blood:	n/a
49	chr15:74495354-74495404	HCT-116	colon:	n/a
50	chr15:74495354-74495404	T-47D	breast:	n/a

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

No.	Distal block	Cell Line	Cell type
1	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
2	chr15:74494443..74497074-chr15:74501503..74504271,2	K562	blood:
3	chr15:74494408..74497236-chr15:74500706..74502894,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC33-1	chr15:74495351-74495439	ENSG00000259264.1
2	lnc-CCDC33-1	chr15:74495046-74495439	ENSG00000259264.1

No data

Variant related genes	Relation type
ENSG00000259264	TF binding region
STRA6	TF binding region
STRA6	CpG island
ENSG00000259264	CpG island
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11630317	0.85[EUR][1000 genomes]
rs11630924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631509	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631944	0.88[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11639090	0.88[EUR][1000 genomes]
rs11639369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11854957	0.88[EUR][1000 genomes]
rs11857410	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899173	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911581	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912258	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12912578	0.89[EUR][1000 genomes]
rs12913041	0.89[EUR][1000 genomes]
rs12915891	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13259	0.88[EUR][1000 genomes]
rs2062309	0.86[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.88[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34147822	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34573746	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35462746	0.87[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848160	0.88[EUR][1000 genomes]
rs3848161	0.88[EUR][1000 genomes]
rs3888004	0.88[EUR][1000 genomes]
rs409856	0.90[EUR][1000 genomes]
rs62003661	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005707	0.88[EUR][1000 genomes]
rs62005709	0.88[EUR][1000 genomes]
rs62005710	0.88[EUR][1000 genomes]
rs62005711	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71399778	0.88[EUR][1000 genomes]
rs72747610	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733163	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8037531	0.87[EUR][1000 genomes]
rs923118	0.88[EUR][1000 genomes]
rs9630417	0.86[EUR][1000 genomes]
rs971755	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971756	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971757	1.00[AMR][1000 genomes];0.99[EUR][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	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74489400-74499000	Weak transcription	Brain Anterior Caudate	brain
3	chr15:74490600-74496200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:74491000-74503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:74492000-74496800	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr15:74492600-74495400	Flanking Active TSS	Placenta	Placenta
7	chr15:74492600-74495400	Enhancers	Right Ventricle	heart
8	chr15:74492600-74495600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:74492600-74495800	Flanking Active TSS	Hela-S3	cervix
10	chr15:74492600-74496200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:74492600-74496400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:74492600-74496400	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr15:74492600-74496600	Enhancers	HMEC	breast
14	chr15:74492600-74496800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:74492600-74497000	Enhancers	Ovary	ovary
16	chr15:74492600-74497000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr15:74492600-74497400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:74492600-74497800	Enhancers	GM12878-XiMat	blood
19	chr15:74492600-74498000	Enhancers	Fetal Lung	lung
20	chr15:74492600-74503200	Enhancers	Fetal Muscle Leg	muscle
21	chr15:74492800-74496600	Enhancers	Fetal Heart	heart
22	chr15:74493000-74496800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr15:74493200-74496800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:74493400-74496800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr15:74493400-74498000	Enhancers	NH-A	brain
26	chr15:74493600-74495800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
27	chr15:74494000-74496400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:74494000-74497400	Weak transcription	Left Ventricle	heart
29	chr15:74494000-74498400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:74494000-74500200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr15:74494200-74495800	Flanking Active TSS	Fetal Intestine Large	intestine
32	chr15:74494200-74496000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:74494200-74496000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr15:74494200-74501000	Weak transcription	HSMM	muscle
35	chr15:74494400-74495400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:74494400-74495400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr15:74494400-74497400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:74494400-74498400	Enhancers	Primary hematopoietic stem cells	blood
39	chr15:74494400-74500200	Enhancers	Fetal Brain Male	brain
40	chr15:74494600-74495400	Enhancers	Brain Germinal Matrix	brain
41	chr15:74494600-74495600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr15:74494600-74495800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:74494600-74495800	Flanking Active TSS	Fetal Intestine Small	intestine
44	chr15:74494600-74496000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:74494600-74496200	Weak transcription	HSMMtube	muscle
46	chr15:74494600-74496200	Enhancers	K562	blood
47	chr15:74494600-74496600	Weak transcription	Esophagus	oesophagus
48	chr15:74494600-74496800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr15:74494600-74496800	Weak transcription	Spleen	Spleen
50	chr15:74494600-74498400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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