Variant report

Variant	rs41269075
Chromosome Location	chr1:45242519-45242520
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:85)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:85 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:45242514-45242676	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr1:45240631-45247540	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:45240526-45248028	GM12892	blood:	n/a	n/a
4	SP1	chr1:45242115-45242585	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:45240641-45242829	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:45240509-45242610	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:45242280-45243426	HUVEC	blood vessel:	n/a	n/a
8	MXI1	chr1:45240490-45242767	IMR90	lung:	n/a	n/a
9	MXI1	chr1:45240438-45242732	SK-N-SH	brain:	n/a	n/a
10	TAF1	chr1:45240498-45242574	K562	blood:	n/a	n/a
11	POLR2A	chr1:45240483-45248016	GM12892	blood:	n/a	n/a
12	POLR2A	chr1:45240295-45248263	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:45240580-45242645	K562	blood:	n/a	n/a
14	TEAD4	chr1:45240428-45242571	K562	blood:	n/a	n/a
15	POLR2A	chr1:45240547-45249219	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:45239529-45250168	SK-N-MC	brain:	n/a	n/a
17	POLR2A	chr1:45240583-45242794	K562	blood:	n/a	n/a
18	POLR2A	chr1:45242512-45242575	MCF-7	breast:	n/a	n/a
19	HEY1	chr1:45240514-45243580	K562	blood:	n/a	n/a
20	MXI1	chr1:45242200-45242574	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:45240637-45242537	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:45240466-45242744	U87	brain:	n/a	n/a
23	CREB1	chr1:45240443-45242534	GM12878	blood:	n/a	n/a
24	MTA3	chr1:45240429-45242843	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:45240503-45242789	K562	blood:	n/a	n/a
26	PAX5	chr1:45242410-45242736	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:45240546-45248272	GM12892	blood:	n/a	n/a
28	PAX5	chr1:45242254-45242794	GM12878	blood:	n/a	chr1:45242336-45242346
29	POLR2A	chr1:45240433-45242751	HL-60	blood:	n/a	n/a
30	POLR2A	chr1:45240631-45243638	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:45240586-45242639	K562	blood:	n/a	n/a
32	UBTF	chr1:45240588-45243134	K562	blood:	n/a	n/a
33	POLR2A	chr1:45240599-45242551	GM12891	blood:	n/a	n/a
34	POLR2A	chr1:45240623-45242553	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:45240491-45242739	GM12891	blood:	n/a	n/a
36	POLR2A	chr1:45240508-45247317	GM12878	blood:	n/a	n/a
37	NR2F2	chr1:45241656-45243726	K562	blood:	n/a	n/a
38	POLR2A	chr1:45240561-45242607	HCT-116	colon:	n/a	n/a
39	POLR2A	chr1:45240667-45242540	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr1:45240713-45247745	PFSK-1	brain:	n/a	n/a
41	POLR2A	chr1:45240530-45242573	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr1:45240522-45242745	IMR90	lung:	n/a	n/a
43	POLR2A	chr1:45240770-45242606	ECC-1	luminal epithelium:	n/a	n/a
44	MYC	chr1:45240459-45242657	K562	blood:	n/a	n/a
45	WRNIP1	chr1:45241897-45242810	GM12878	blood:	n/a	n/a
46	POLR2A	chr1:45240271-45247480	K562	blood:	n/a	n/a
47	POLR2A	chr1:45240399-45242658	HUVEC	blood vessel:	n/a	n/a
48	PAX5	chr1:45242454-45242739	GM12878	blood:	n/a	n/a
49	SMARCB1	chr1:45240833-45242676	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr1:45240431-45242805	HCT-116	colon:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45239429..45243402-chr1:45282541..45287001,15	MCF-7	breast:
2	chr1:45240326..45242675-chr1:45804232..45807042,4	K562	blood:
3	chr1:45194515..45198714-chr1:45239955..45244261,13	MCF-7	breast:
4	chr1:45239877..45242890-chr1:45804203..45807042,4	K562	blood:
5	chr1:45239905..45242727-chr1:45449975..45452356,2	K562	blood:
6	chr1:45204011..45207083-chr1:45240823..45243671,4	MCF-7	breast:
7	chr1:45196722..45198630-chr1:45239788..45242584,2	MCF-7	breast:
8	chr1:45241279..45243837-chr1:45275916..45278923,3	MCF-7	breast:
9	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
10	chr1:45239592..45244618-chr1:45476667..45480609,10	K562	blood:
11	chr1:45239135..45244789-chr1:45475459..45482236,15	K562	blood:
12	chr1:45240574..45242536-chr17:56734764..56737009,2	MCF-7	breast:
13	chr1:45239518..45243020-chr1:45264375..45267077,6	MCF-7	breast:
14	chr1:45239737..45242586-chr1:45965500..45967251,2	K562	blood:
15	chr1:45240714..45243157-chr1:45476342..45480108,4	MCF-7	breast:
16	chr1:45239609..45242950-chr1:45264036..45267552,6	MCF-7	breast:
17	chr1:45240022..45242639-chr1:45267540..45269350,2	MCF-7	breast:
18	chr1:45185509..45188442-chr1:45240940..45242560,2	MCF-7	breast:
19	chr1:45241739..45242522-chr3:33481472..33482173,2	Hela-S3	cervix:
20	chr1:45239959..45246724-chr1:45282430..45287057,13	MCF-7	breast:
21	chr1:45211016..45213726-chr1:45240164..45242830,2	MCF-7	breast:
22	chr1:45240107..45242701-chr1:46047468..46050316,4	K562	blood:
23	chr1:45239942..45244585-chr1:45273690..45277023,5	MCF-7	breast:

No data

Variant related genes	Relation type
SNORD38B	TF binding region
ENSG00000225721	TF binding region
RPS8	TF binding region
SNORD38A	TF binding region
ENSG00000188396	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000173846	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000222009	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000117425	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000153560	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000202444	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10127901	1.00[EUR][1000 genomes]
rs11573544	0.83[ASN][1000 genomes]
rs11573571	1.00[ASN][1000 genomes]
rs12072767	1.00[ASN][1000 genomes]
rs263958	0.83[ASN][1000 genomes]
rs3738249	0.83[ASN][1000 genomes]
rs41269093	1.00[ASN][1000 genomes]
rs41311199	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv998871	chr1:45196587-45251179	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	171 gene(s)	inside rSNPs	diseases
8	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
10	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
11	nsv947252	chr1:45242176-45258816	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45240400-45242800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:45240400-45242800	Active TSS	Fetal Kidney	kidney
3	chr1:45240400-45242800	Active TSS	HSMMtube	muscle
4	chr1:45240400-45242800	Active TSS	NHDF-Ad	bronchial
5	chr1:45240400-45243000	Active TSS	Psoas Muscle	Psoas
6	chr1:45240400-45243000	Active TSS	HSMM	muscle
7	chr1:45240600-45242600	Active TSS	Ovary	ovary
8	chr1:45240600-45242800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr1:45240600-45244000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:45240800-45243600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:45241000-45242600	Transcr. at gene 5' and 3'	Right Atrium	heart
12	chr1:45241600-45242600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:45241600-45242600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr1:45241600-45242800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:45241600-45243000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
16	chr1:45241600-45243600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
17	chr1:45241600-45243800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
18	chr1:45241600-45244200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
19	chr1:45241600-45244200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr1:45241600-45244200	Transcr. at gene 5' and 3'	NHEK	skin
21	chr1:45241600-45244600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
22	chr1:45241600-45244600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
23	chr1:45241600-45244600	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr1:45241600-45244800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:45241800-45242600	Transcr. at gene 5' and 3'	Primary B cells from peripheral blood	blood
26	chr1:45241800-45242600	Flanking Active TSS	Primary hematopoietic stem cells	blood
27	chr1:45241800-45242600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr1:45241800-45242600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
29	chr1:45241800-45242800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr1:45241800-45242800	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
31	chr1:45241800-45243000	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
32	chr1:45241800-45243000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:45241800-45243200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:45241800-45243200	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:45241800-45243200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
36	chr1:45241800-45243200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
37	chr1:45241800-45243400	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:45241800-45243600	Transcr. at gene 5' and 3'	Right Ventricle	heart
39	chr1:45241800-45243600	Transcr. at gene 5' and 3'	Osteobl	bone
40	chr1:45241800-45244000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
41	chr1:45241800-45244200	Transcr. at gene 5' and 3'	NHLF	lung
42	chr1:45241800-45244800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:45241800-45244800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:45241800-45244800	Transcr. at gene 5' and 3'	A549	lung
45	chr1:45241800-45244800	Transcr. at gene 5' and 3'	K562	blood
46	chr1:45241800-45245000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
47	chr1:45242000-45242600	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
48	chr1:45242000-45242600	Flanking Active TSS	Liver	Liver
49	chr1:45242000-45242600	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr1:45242000-45242600	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain

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