Variant report

Variant	rs2411284
Chromosome Location	chr15:44038899-44038900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:210)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:210 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:44038820-44038970	SAEC	small airway:	n/a	n/a
2	POLR2A	chr15:44037798-44040385	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr15:44038091-44039442	GM12878	blood:	n/a	n/a
4	POLR2A	chr15:44037988-44039589	GM12891	blood:	n/a	n/a
5	POLR2A	chr15:44037659-44039562	HepG2	liver:	n/a	n/a
6	TAF7	chr15:44038384-44039067	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr15:44038780-44038930	GM12864	blood:	n/a	n/a
8	JUND	chr15:44038809-44039028	H1-hESC	embryonic stem cell:	n/a	n/a
9	RCOR1	chr15:44038066-44039602	K562	blood:	n/a	n/a
10	BHLHE40	chr15:44038444-44039446	K562	blood:	n/a	n/a
11	YY1	chr15:44038105-44038924	HepG2	liver:	n/a	n/a
12	POLR2A	chr15:44038200-44039092	HepG2	liver:	n/a	n/a
13	ETS1	chr15:44038842-44039107	K562	blood:	n/a	n/a
14	HCFC1	chr15:44037948-44039522	Hela-S3	cervix:	n/a	n/a
15	SIN3A	chr15:44038092-44039000	GM12878	blood:	n/a	n/a
16	MAX	chr15:44038752-44038987	SK-N-SH	brain:	n/a	n/a
17	TAF1	chr15:44038183-44039210	HepG2	liver:	n/a	n/a
18	UBTF	chr15:44038160-44039594	K562	blood:	n/a	n/a
19	REST	chr15:44038388-44038959	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr15:44038106-44039515	GM12878	blood:	n/a	n/a
21	TBP	chr15:44038358-44039551	K562	blood:	n/a	n/a
22	POLR2A	chr15:44037989-44039606	H1-hESC	embryonic stem cell:	n/a	n/a
23	MXI1	chr15:44037950-44040063	SK-N-SH	brain:	n/a	n/a
24	STAT5A	chr15:44038406-44038908	GM12878	blood:	n/a	n/a
25	NFIC	chr15:44038405-44039031	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:44038202-44039432	GM12892	blood:	n/a	n/a
27	CTCF	chr15:44038820-44038970	Hela-S3	cervix:	n/a	n/a
28	MAX	chr15:44038292-44039002	A549	lung:	n/a	n/a
29	SPI1	chr15:44038884-44039489	GM12878	blood:	n/a	chr15:44039299-44039312
30	ZNF143	chr15:44038838-44039003	H1-hESC	embryonic stem cell:	n/a	n/a
31	YY1	chr15:44038197-44039094	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr15:44038179-44039345	HUVEC	blood vessel:	n/a	n/a
33	EGR1	chr15:44038801-44039184	K562	blood:	n/a	n/a
34	TAF1	chr15:44038238-44038932	HepG2	liver:	n/a	n/a
35	POLR2A	chr15:44038113-44039583	PBDE	blood:	n/a	n/a
36	CTCF	chr15:44038780-44038930	GM12871	blood:	n/a	n/a
37	TAF1	chr15:44038126-44039400	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZBTB7A	chr15:44038861-44039115	K562	blood:	n/a	n/a
39	TAF1	chr15:44038280-44038959	A549	lung:	n/a	n/a
40	POLR2A	chr15:44038094-44039402	MCF10A-Er-Src	breast:	n/a	n/a
41	MAX	chr15:44038227-44039035	HCT-116	colon:	n/a	n/a
42	EGR1	chr15:44038796-44039137	H1-hESC	embryonic stem cell:	n/a	n/a
43	MYC	chr15:44038492-44039002	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr15:44038800-44038950	SAEC	small airway:	n/a	n/a
45	CTCF	chr15:44038760-44038910	GM12872	blood:	n/a	n/a
46	POLR2A	chr15:44038152-44038970	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr15:44037893-44039571	GM12892	blood:	n/a	n/a
48	POLR2A	chr15:44038263-44039104	K562	blood:	n/a	n/a
49	POLR2A	chr15:44038289-44039460	GM12891	blood:	n/a	n/a
50	MAX	chr15:44038250-44039036	ECC-1	luminal epithelium:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:44038871-44038921	SAEC	small airway:	n/a
2	chr15:44038871-44038921	NHDF-neo	bronchial:	n/a
3	chr15:44038871-44038921	IMR90	lung:	fetal
4	chr15:44038871-44038921	U87	brain:	n/a
5	chr15:44038871-44038921	HRCEpiC	kidney:	n/a
6	chr15:44038871-44038921	PANC-1	pancreas:	n/a
7	chr15:44038871-44038921	HIPEpiC	eye:	n/a
8	chr15:44038871-44038921	NT2-D1	testis:	n/a
9	chr15:44038871-44038921	HCT-116	colon:	n/a
10	chr15:44038871-44038921	GM12891	blood:	n/a
11	chr15:44038871-44038921	BJ	skin:	n/a
12	chr15:44038871-44038921	MCF-7	breast:	n/a
13	chr15:44038871-44038921	NB4	blood:	n/a
14	chr15:44038871-44038921	HEK293	kidney:	embryo
15	chr15:44038871-44038921	HepG2	liver:	n/a
16	chr15:44038871-44038921	HCM	heart:	n/a
17	chr15:44038871-44038921	AG09309	skin:	n/a
18	chr15:44038871-44038921	ECC-1	luminal epithelium:	n/a
19	chr15:44038871-44038921	H1-hESC	embryonic stem cell:	embryo
20	chr15:44038871-44038921	GM19239	blood:	n/a
21	chr15:44038871-44038921	AG09319	gingival:	n/a
22	chr15:44038871-44038921	AoSMC	blood vessel:	n/a
23	chr15:44038871-44038921	HRPEpiC	eye:	n/a
24	chr15:44038871-44038921	HEEpiC	esophagus:	n/a
25	chr15:44038871-44038921	NHBE	bronchial:	n/a
26	chr15:44038871-44038921	HAEpiC	amniotic membrane:	n/a
27	chr15:44038871-44038921	CMK	blood:	n/a
28	chr15:44038871-44038921	AG10803	skin:	n/a
29	chr15:44038871-44038921	MCF10A-Er-Src	breast:	n/a
30	chr15:44038871-44038921	HL-60	blood:	n/a
31	chr15:44038871-44038921	Hela-S3	cervix:	n/a
32	chr15:44038871-44038921	AG04449	skin:	fetal
33	chr15:44038871-44038921	Hepatocyte	liver:	n/a
34	chr15:44038871-44038921	SK-N-SH	brain:	n/a
35	chr15:44038871-44038921	ProgFib	skin:	n/a
36	chr15:44038871-44038921	NH-A	brain:	n/a
37	chr15:44038871-44038921	BE2_C	brain:	n/a
38	chr15:44038871-44038921	HRE	kidney:	n/a
39	chr15:44038871-44038921	SK-N-MC	brain:	n/a
40	chr15:44038871-44038921	HNPCEpiC	eye:	n/a
41	chr15:44038871-44038921	GM06990	blood:	n/a
42	chr15:44038871-44038921	T-47D	breast:	n/a
43	chr15:44038871-44038921	LNCaP	prostate:	n/a
44	chr15:44038871-44038921	GM12878	blood:	n/a
45	chr15:44038871-44038921	RPTEC	kidney:	n/a
46	chr15:44038871-44038921	A549	lung:	n/a
47	chr15:44038871-44038921	ovcar-3	ovarian:	n/a
48	chr15:44038871-44038921	PFSK-1	brain:	n/a
49	chr15:44038871-44038921	HPAEpiC	pulmonary alveolar:	n/a
50	chr15:44038871-44038921	AG04450	lung:	fetal

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

No.	Distal block	Cell Line	Cell type
1	chr15:44038515..44039093-chr16:56965918..56966473,2	Hela-S3	cervix:
2	chr15:44038318..44039246-chr17:41465388..41466312,2	Hela-S3	cervix:
3	chr11:76494689..76495371-chr15:44038517..44039029,2	Hela-S3	cervix:
4	chr15:44038791..44041212-chr15:44089540..44091517,2	MCF-7	breast:
5	chr15:44037743..44040701-chr15:44068299..44070156,3	MCF-7	breast:
6	chr15:44036424..44040091-chr15:44115436..44119319,5	K562	blood:
7	chr15:44036424..44040091-chr15:44116705..44119319,4	K562	blood:
8	chr15:44038318..44039268-chr6:109703161..109703718,2	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STRC-1	chr15:44038729-44039292	NONHSAT042114
2	lnc-SERF2-3	chr15:44038608-44038904	NONHSAT042119

No data

Variant related genes	Relation type
CATSPER2P1	TF binding region
CATSPER2P1	CpG island
ENSG00000128886	Chromatin interaction
ENSG00000051108	Chromatin interaction
ENSG00000182704	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000092470	Chromatin interaction
ENSG00000140259	Chromatin interaction
ENSG00000140264	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000184716	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1053492	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11070410	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070412	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11638972	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12908467	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1975364	0.84[EUR][1000 genomes]
rs2447215	0.80[AFR][1000 genomes]
rs2470135	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2927085	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2955969	0.84[EUR][1000 genomes]
rs3087657	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35654783	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35866764	0.84[EUR][1000 genomes]
rs4332723	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4617832	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924720	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924722	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs575082	0.84[EUR][1000 genomes]
rs62018947	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62018952	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs663214	0.87[EUR][1000 genomes]
rs693919	0.83[EUR][1000 genomes]
rs694461	0.85[EUR][1000 genomes]
rs7174732	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7175129	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7178343	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7180818	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72714307	0.94[ASN][1000 genomes]
rs8033846	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8033995	0.96[ASN][1000 genomes]
rs8034451	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv904150	chr15:43836478-44040965	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv904158	chr15:43852043-44053617	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
9	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
10	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription 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 miRNA target site	90 gene(s)	inside rSNPs	diseases
11	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
12	nsv976928	chr15:43948866-44040886	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS 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	154 gene(s)	inside rSNPs	diseases
14	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2411284	AC011330.5	cis	Artery Tibial	GTEx
rs2411284	ZSCAN29	cis	Thyroid	GTEx
rs2411284	AC011330.5	cis	Thyroid	GTEx
rs2411284	STRCP1	cis	Whole Blood	GTEx
rs2411284	STRCP1	cis	Thyroid	GTEx
rs2411284	CKMT1A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44037000-44040200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr15:44037400-44039800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:44037800-44039000	Active TSS	HepG2	liver
4	chr15:44037800-44039800	Active TSS	Brain Angular Gyrus	brain
5	chr15:44037800-44040000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:44037800-44040000	Active TSS	Brain Anterior Caudate	brain
7	chr15:44037800-44040000	Active TSS	Fetal Brain Female	brain
8	chr15:44037800-44040000	Active TSS	NHEK	skin
9	chr15:44037800-44040000	Active TSS	Osteobl	bone
10	chr15:44037800-44040200	Active TSS	Brain Hippocampus Middle	brain
11	chr15:44037800-44040200	Active TSS	Hela-S3	cervix
12	chr15:44037800-44040400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:44037800-44040600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:44037800-44040600	Active TSS	Psoas Muscle	Psoas
15	chr15:44037800-44040600	Active TSS	Stomach Smooth Muscle	stomach
16	chr15:44037800-44040600	Active TSS	HSMM	muscle
17	chr15:44037800-44041000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr15:44037800-44041000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:44037800-44041200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:44037800-44041800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:44037800-44042000	Active TSS	Colonic Mucosa	Colon
22	chr15:44037800-44042200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:44038000-44039400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr15:44038000-44039400	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr15:44038000-44039600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr15:44038000-44039600	Active TSS	Colon Smooth Muscle	Colon
27	chr15:44038000-44039600	Active TSS	Gastric	stomach
28	chr15:44038000-44039600	Active TSS	Left Ventricle	heart
29	chr15:44038000-44039600	Active TSS	Lung	lung
30	chr15:44038000-44039600	Active TSS	Pancreas	Pancrea
31	chr15:44038000-44039600	Active TSS	Sigmoid Colon	Sigmoid Colon
32	chr15:44038000-44039800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:44038000-44039800	Active TSS	Stomach Mucosa	stomach
34	chr15:44038000-44040000	Active TSS	H1 Cell Line	embryonic stem cell
35	chr15:44038000-44040000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:44038000-44040000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:44038000-44040000	Active TSS	Primary T cells from cord blood	blood
38	chr15:44038000-44040000	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr15:44038000-44040000	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr15:44038000-44040000	Active TSS	Liver	Liver
41	chr15:44038000-44040000	Active TSS	Duodenum Mucosa	Duodenum
42	chr15:44038000-44040000	Active TSS	Fetal Lung	lung
43	chr15:44038000-44040000	Active TSS	Fetal Muscle Leg	muscle
44	chr15:44038000-44040000	Active TSS	Fetal Stomach	stomach
45	chr15:44038000-44040200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:44038000-44040200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:44038000-44040200	Active TSS	Aorta	Aorta
48	chr15:44038000-44040200	Active TSS	Brain Inferior Temporal Lobe	brain
49	chr15:44038000-44040200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr15:44038000-44040200	Active TSS	Esophagus	oesophagus

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