Variant report

Variant	rs41311199
Chromosome Location	chr1:45266592-45266593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr1:45265328-45266640	HepG2	liver:	n/a	chr1:45265665-45265680
2	SMARCB1	chr1:45265360-45266787	Hela-S3	cervix:	n/a	n/a
3	YY1	chr1:45265274-45266777	GM12892	blood:	n/a	chr1:45265847-45265861
4	MAX	chr1:45266442-45266933	SK-N-SH	brain:	n/a	n/a
5	JUN	chr1:45265161-45266896	K562	blood:	n/a	n/a
6	MXI1	chr1:45265270-45266876	IMR90	lung:	n/a	chr1:45265665-45265680
7	GATA2	chr1:45266583-45266878	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:45265301-45266849	K562	blood:	n/a	n/a
9	CHD1	chr1:45265265-45266961	IMR90	lung:	n/a	chr1:45265863-45265873 chr1:45266636-45266646
10	POLR2A	chr1:45265395-45266652	GM15510	blood:	n/a	n/a
11	HMGN3	chr1:45265381-45266768	K562	blood:	n/a	n/a
12	E2F6	chr1:45266489-45266824	K562	blood:	n/a	n/a
13	POLR2A	chr1:45265253-45266703	HCT-116	colon:	n/a	n/a
14	HEY1	chr1:45266529-45266788	K562	blood:	n/a	n/a
15	GATA2	chr1:45266396-45266903	SH-SY5Y	brain:	n/a	n/a
16	CREB1	chr1:45265371-45266658	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:45265331-45266621	GM12878	blood:	n/a	n/a
18	MXI1	chr1:45266591-45266730	K562	blood:	n/a	n/a
19	RAD21	chr1:45265233-45266636	HCT-116	colon:	n/a	chr1:45266471-45266481 chr1:45265801-45265814
20	POLR2A	chr1:45265415-45266805	IMR90	lung:	n/a	n/a
21	MAX	chr1:45265175-45266717	A549	lung:	n/a	chr1:45265561-45265568 chr1:45265623-45265633
22	MAX	chr1:45265325-45266735	Hela-S3	cervix:	n/a	chr1:45265561-45265568 chr1:45265623-45265633
23	POLR2A	chr1:45265432-45266816	HUVEC	blood vessel:	n/a	n/a
24	MAX	chr1:45265363-45266603	HepG2	liver:	n/a	chr1:45265561-45265568 chr1:45265623-45265633
25	POLR2A	chr1:45265387-45266615	GM12892	blood:	n/a	n/a
26	CHD2	chr1:45266528-45266663	H1-hESC	embryonic stem cell:	n/a	chr1:45266636-45266646
27	POLR2A	chr1:45265234-45266720	U87	brain:	n/a	n/a
28	YY1	chr1:45265297-45266757	K562	blood:	n/a	chr1:45265847-45265861
29	POLR2A	chr1:45265285-45266862	HL-60	blood:	n/a	n/a
30	SIN3AK20	chr1:45265296-45266742	PANC-1	pancreas:	n/a	n/a
31	HEY1	chr1:45265268-45266874	K562	blood:	n/a	chr1:45265852-45265867 chr1:45265618-45265633 chr1:45265843-45265858
32	MYC	chr1:45266582-45266677	MCF-7	breast:	n/a	n/a
33	CHD2	chr1:45266584-45266743	GM12878	blood:	n/a	chr1:45266636-45266646
34	MAX	chr1:45266516-45266727	K562	blood:	n/a	n/a
35	POLR2A	chr1:45265321-45266746	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:45266512-45266637	H1-hESC	embryonic stem cell:	n/a	n/a
37	RAD21	chr1:45265155-45266869	SK-N-SH	brain:	n/a	chr1:45266471-45266481 chr1:45265801-45265814
38	POLR2A	chr1:45265335-45266847	GM12878	blood:	n/a	n/a
39	RCOR1	chr1:45266516-45266727	K562	blood:	n/a	n/a
40	CTBP2	chr1:45265360-45266813	H1-hESC	embryonic stem cell:	n/a	n/a
41	E2F6	chr1:45265319-45266787	K562	blood:	n/a	chr1:45265870-45265879
42	PAX5	chr1:45265383-45266603	GM12892	blood:	n/a	n/a
43	UBTF	chr1:45265411-45266758	K562	blood:	n/a	n/a
44	POLR2A	chr1:45265504-45266753	MCF10A-Er-Src	breast:	n/a	n/a
45	HCFC1	chr1:45265177-45266977	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:45265287-45266811	H1-neurons	neurons:	n/a	n/a
47	MTA3	chr1:45265208-45266896	GM12878	blood:	n/a	n/a
48	ETS1	chr1:45266426-45266833	K562	blood:	n/a	n/a
49	POLR2A	chr1:45265294-45266880	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr1:45265240-45266873	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45205245..45207359-chr1:45265556..45268016,2	MCF-7	breast:
2	chr1:45264279..45267905-chr1:45476139..45480748,9	K562	blood:
3	chr1:45194731..45198369-chr1:45262951..45267593,8	MCF-7	breast:
4	chr1:45186012..45189065-chr1:45262922..45268915,8	MCF-7	breast:
5	chr1:45239518..45243020-chr1:45264375..45267077,6	MCF-7	breast:
6	chr1:45265977..45266790-chr15:50715807..50716660,2	NB4	blood:
7	chr1:45262923..45267744-chr1:45767225..45772183,8	K562	blood:
8	chr1:45138566..45141370-chr1:45265919..45267652,2	K562	blood:
9	chr1:45194156..45199355-chr1:45264282..45268731,9	MCF-7	breast:
10	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
11	chr1:45265558..45267516-chr1:45964222..45967034,2	K562	blood:
12	chr1:45239609..45242950-chr1:45264036..45267552,6	MCF-7	breast:
13	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
14	chr1:45264355..45267553-chr1:45476139..45481796,8	K562	blood:
15	chr1:45266069..45266767-chr5:151150725..151151366,2	HCT-116	colon:
16	chr1:45264684..45267553-chr1:45478723..45482931,4	MCF-7	breast:
17	chr1:45210802..45212965-chr1:45265931..45268698,2	K562	blood:
18	chr1:45248852..45254229-chr1:45263166..45267959,10	MCF-7	breast:
19	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:

Variant related genes	Relation type
PLK3	TF binding region
ENSG00000207421	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000126106	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000126107	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
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]
rs41269075	1.00[ASN][1000 genomes]
rs41269093	1.00[ASN][1000 genomes]
rs9988624	1.00[EUR][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	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	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
8	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
9	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
10	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
11	nsv871320	chr1:45259295-45274841	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	58 gene(s)	inside rSNPs	diseases
12	nsv870773	chr1:45259295-45287306	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases
13	nsv870876	chr1:45264545-45273531	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	56 gene(s)	inside rSNPs	diseases
14	nsv546147	chr1:45264874-45271097	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	44 gene(s)	inside rSNPs	diseases
15	esv3404071	chr1:45264890-45267738	Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45265200-45266600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:45265200-45266600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:45265200-45266600	Active TSS	Fetal Lung	lung
4	chr1:45265200-45267200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:45265200-45267200	Active TSS	Fetal Kidney	kidney
6	chr1:45265200-45267600	Active TSS	Primary T cells from cord blood	blood
7	chr1:45265200-45267600	Active TSS	Brain Angular Gyrus	brain
8	chr1:45265200-45267600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:45265200-45267600	Active TSS	Brain Substantia Nigra	brain
10	chr1:45265200-45267600	Active TSS	Fetal Brain Female	brain
11	chr1:45265200-45267600	Active TSS	Rectal Smooth Muscle	rectum
12	chr1:45265200-45267600	Active TSS	Right Ventricle	heart
13	chr1:45265200-45267600	Active TSS	Thymus	Thymus
14	chr1:45265200-45267600	Active TSS	HSMM	muscle
15	chr1:45265200-45267800	Active TSS	Colon Smooth Muscle	Colon
16	chr1:45265200-45268200	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr1:45265400-45266600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:45265400-45266600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:45265400-45266600	Active TSS	GM12878-XiMat	blood
20	chr1:45265400-45266600	Active TSS	HepG2	liver
21	chr1:45265400-45266800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:45265400-45267200	Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr1:45265400-45267200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr1:45265400-45267200	Active TSS	Brain Cingulate Gyrus	brain
25	chr1:45265400-45267200	Active TSS	NHEK	skin
26	chr1:45265400-45267400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr1:45265400-45267400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr1:45265400-45267400	Active TSS	Fetal Intestine Large	intestine
29	chr1:45265400-45267600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr1:45265400-45267600	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr1:45265400-45267600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:45265400-45267600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:45265400-45267600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:45265400-45267600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:45265400-45267600	Active TSS	Primary T killer memory cells from peripheral blood	blood
36	chr1:45265400-45267600	Active TSS	Muscle Satellite Cultured Cells	--
37	chr1:45265400-45267600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr1:45265400-45267600	Active TSS	Esophagus	oesophagus
39	chr1:45265400-45267600	Active TSS	Left Ventricle	heart
40	chr1:45265400-45267600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr1:45265400-45267600	Active TSS	A549	lung
42	chr1:45265400-45267600	Active TSS	Hela-S3	cervix
43	chr1:45265400-45267600	Active TSS	Osteobl	bone
44	chr1:45265600-45266600	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:45265600-45266600	Active TSS	Liver	Liver
46	chr1:45265600-45266600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
47	chr1:45265600-45266600	Active TSS	Stomach Mucosa	stomach
48	chr1:45265600-45266600	Active TSS	Spleen	Spleen
49	chr1:45265600-45266800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:45265600-45266800	Active TSS	Primary T cells fromperipheralblood	blood

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