Variant report

Variant	rs41266630
Chromosome Location	chr1:151042936-151042937
allele	A/G
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	POLR2A	chr1:151042718-151043938	A549	lung:	n/a	n/a
2	HA-E2F1	chr1:151042767-151043451	Hela-S3	cervix:	n/a	chr1:151042962-151042973 chr1:151042962-151042973 chr1:151042961-151042972 chr1:151042959-151042976
3	TAL1	chr1:151042695-151043875	K562	blood:	n/a	n/a
4	CTCF	chr1:151042930-151043074	H1-hESC	embryonic stem cell:	n/a	chr1:151042992-151043001
5	MAZ	chr1:151042744-151043885	Hela-S3	cervix:	n/a	n/a
6	MTA3	chr1:151042554-151044152	GM12878	blood:	n/a	n/a
7	PML	chr1:151042465-151044102	GM12878	blood:	n/a	n/a
8	GTF2F1	chr1:151042779-151043548	K562	blood:	n/a	n/a
9	CEBPB	chr1:151042761-151043435	H1-hESC	embryonic stem cell:	n/a	n/a
10	SIN3AK20	chr1:151042675-151043873	A549	lung:	n/a	n/a
11	MXI1	chr1:151042742-151043823	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr1:151042620-151043881	H1-hESC	embryonic stem cell:	n/a	n/a
13	MYC	chr1:151042823-151043564	K562	blood:	n/a	n/a
14	MAX	chr1:151042635-151043971	ECC-1	luminal epithelium:	n/a	n/a
15	RAD21	chr1:151042763-151043953	H1-hESC	embryonic stem cell:	n/a	chr1:151042988-151042998 chr1:151043693-151043706 chr1:151043690-151043709
16	YY1	chr1:151042782-151043921	H1-hESC	embryonic stem cell:	n/a	chr1:151043647-151043658 chr1:151043701-151043710 chr1:151043698-151043707 chr1:151043747-151043758
17	USF2	chr1:151042795-151043431	GM12878	blood:	n/a	n/a
18	BHLHE40	chr1:151042701-151043834	K562	blood:	n/a	n/a
19	YY1	chr1:151042561-151043855	SK-N-SH	brain:	n/a	chr1:151043647-151043658 chr1:151043701-151043710 chr1:151043698-151043707 chr1:151043747-151043758
20	CTCF	chr1:151042920-151043070	AG09309	skin:	n/a	chr1:151042992-151043001
21	NR3C1	chr1:151042775-151043391	A549	lung:	n/a	n/a
22	CTCF	chr1:151042816-151043916	K562	blood:	n/a	chr1:151043691-151043712 chr1:151042992-151043001 chr1:151043692-151043701 chr1:151043694-151043704 chr1:151043689-151043707 chr1:151043692-151043705 chr1:151043690-151043706 chr1:151043692-151043705
23	RUNX3	chr1:151042659-151043934	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:151042665-151043886	GM18526	blood:	n/a	n/a
25	EP300	chr1:151042753-151043907	K562	blood:	n/a	chr1:151043698-151043707
26	E2F1	chr1:151042766-151043474	Hela-S3	cervix:	n/a	chr1:151042962-151042973 chr1:151042962-151042973 chr1:151042961-151042972 chr1:151042965-151042973 chr1:151042959-151042976
27	BCLAF1	chr1:151042641-151043923	GM12878	blood:	n/a	chr1:151043699-151043708 chr1:151043679-151043688 chr1:151043037-151043046
28	IRF4	chr1:151042768-151043317	GM12878	blood:	n/a	n/a
29	YY1	chr1:151042787-151043386	HCT-116	colon:	n/a	n/a
30	CTCF	chr1:151042920-151043070	GM12865	blood:	n/a	chr1:151042992-151043001
31	TEAD4	chr1:151042564-151043856	K562	blood:	n/a	n/a
32	MAX	chr1:151042644-151044025	MCF-7	breast:	n/a	n/a
33	E2F4	chr1:151042761-151043264	GM12878	blood:	n/a	chr1:151042962-151042973 chr1:151042962-151042973 chr1:151042965-151042973 chr1:151042959-151042976
34	POLR2A	chr1:151042749-151043660	A549	lung:	n/a	n/a
35	POLR2A	chr1:151042668-151043930	ECC-1	luminal epithelium:	n/a	n/a
36	PBX3	chr1:151042864-151043216	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:151042599-151043865	GM12891	blood:	n/a	n/a
38	TAF1	chr1:151042794-151043357	PFSK-1	brain:	n/a	n/a
39	STAT3	chr1:151042739-151043171	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:151041429-151044042	PANC-1	pancreas:	n/a	n/a
41	CTCF	chr1:151042880-151043030	HCT-116	colon:	n/a	chr1:151042992-151043001
42	REST	chr1:151042740-151043586	A549	lung:	n/a	n/a
43	CREB1	chr1:151042829-151043574	ECC-1	luminal epithelium:	n/a	n/a
44	MYC	chr1:151042852-151043320	Hela-S3	cervix:	n/a	n/a
45	ZNF143	chr1:151042824-151043857	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAZ	chr1:151042713-151043975	GM12878	blood:	n/a	n/a
47	CTCF	chr1:151042920-151043070	WERI-Rb-1	eye:	n/a	chr1:151042992-151043001
48	IRF1	chr1:151042728-151043866	K562	blood:	n/a	chr1:151043457-151043470 chr1:151043458-151043472
49	ZNF143	chr1:151042838-151043897	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:151042487-151043892	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150550567..150552845-chr1:151042071..151045056,2	MCF-7	breast:
2	chr1:151042724..151043226-chr1:207924659..207925559,2	HCT-116	colon:
3	chr1:151042356..151044958-chr1:151252271..151256325,4	K562	blood:
4	chr1:150977392..150983338-chr1:151040807..151046211,16	MCF-7	breast:
5	chr1:149856233..149859163-chr1:151041177..151043443,2	MCF-7	breast:
6	chr1:150996741..150997636-chr1:151042895..151043878,5	MCF-7	breast:
7	chr1:68150474..68151377-chr1:151042815..151043553,2	HCT-116	colon:
8	chr1:151042193..151044467-chr1:151761804..151763901,2	MCF-7	breast:
9	chr1:150995604..150998641-chr1:151041475..151044833,5	MCF-7	breast:
10	chr1:150532621..150534705-chr1:151041557..151045135,3	K562	blood:
11	chr1:151042666..151043354-chr11:62609073..62609628,2	Hela-S3	cervix:
12	chr1:150970397..150973154-chr1:151042388..151043902,2	MCF-7	breast:
13	chr1:151041073..151043333-chr1:151126816..151129566,2	K562	blood:
14	chr1:150978624..150980808-chr1:151042705..151044650,2	MCF-7	breast:
15	chr1:150952337..150955570-chr1:151040233..151043325,3	MCF-7	breast:
16	chr1:151041779..151043840-chr1:151166772..151169795,3	MCF-7	breast:
17	chr1:150978947..150982308-chr1:151041500..151045951,4	K562	blood:
18	chr1:150943930..150948676-chr1:151041268..151044275,5	MCF-7	breast:
19	chr1:151042779..151043609-chr6:26157678..26158524,3	Hela-S3	cervix:
20	chr1:151040998..151044328-chr1:151135769..151140484,5	MCF-7	breast:
21	chr1:151042160..151045059-chr1:151225748..151228568,3	MCF-7	breast:
22	chr1:151042761..151043522-chr2:174829863..174830820,2	Hela-S3	cervix:
23	chr1:144533779..144534373-chr1:151042569..151043561,2	Hela-S3	cervix:
24	chr1:151041683..151045028-chr1:151160226..151163233,4	MCF-7	breast:
25	chr1:150944568..150948169-chr1:151041647..151044581,4	MCF-7	breast:
26	chr1:151040013..151045011-chr1:151111761..151118476,6	MCF-7	breast:
27	chr1:151042151..151045476-chr1:151127754..151130933,3	MCF-7	breast:
28	chr1:151042897..151044564-chr1:151161784..151163721,2	MCF-7	breast:
29	chr1:151042255..151044217-chr1:151136884..151138558,2	MCF-7	breast:
30	chr1:151042679..151043583-chr12:52445059..52445817,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CDC42SE1-1	chr1:151040975-151043079	NONHSAT006357

Variant related genes	Relation type
CDC42SE1	TF binding region
GABPB2	TF binding region
ENSG00000203288	Chromatin interaction
ENSG00000117335	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000182134	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000116717	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000172845	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000143412	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs41266626	0.83[EUR][1000 genomes]
rs41267548	1.00[EUR][1000 genomes]
rs41310905	1.00[EUR][1000 genomes]
rs57330524	1.00[EUR][1000 genomes]
rs74125065	1.00[EUR][1000 genomes]
rs74125077	1.00[EUR][1000 genomes]
rs74125079	1.00[EUR][1000 genomes]
rs74125080	1.00[EUR][1000 genomes]
rs74125087	1.00[EUR][1000 genomes]
rs74125093	1.00[EUR][1000 genomes]
rs74127505	1.00[EUR][1000 genomes]
rs74127529	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 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	chr1:151042200-151043200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:151042200-151043400	Weak transcription	HepG2	liver
3	chr1:151042200-151043600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:151042200-151043800	Active TSS	Adipose Nuclei	Adipose
5	chr1:151042200-151044000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr1:151042200-151044200	Active TSS	Colon Smooth Muscle	Colon
7	chr1:151042200-151044600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:151042400-151043000	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr1:151042400-151043000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr1:151042400-151043000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:151042400-151043000	Flanking Active TSS	Dnd41	blood
12	chr1:151042400-151043200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr1:151042400-151044000	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr1:151042400-151044000	Active TSS	Primary T cells from cord blood	blood
15	chr1:151042400-151044000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr1:151042400-151044000	Active TSS	Fetal Intestine Large	intestine
17	chr1:151042400-151044000	Active TSS	Thymus	Thymus
18	chr1:151042400-151044200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:151042400-151044200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:151042400-151044200	Active TSS	Brain Substantia Nigra	brain
21	chr1:151042400-151044200	Active TSS	Pancreas	Pancrea
22	chr1:151042400-151044400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:151042400-151044600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:151042400-151044600	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:151042600-151043000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:151042600-151043000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr1:151042600-151043000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr1:151042600-151043000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr1:151042600-151043000	Flanking Active TSS	HMEC	breast
30	chr1:151042600-151043000	Flanking Active TSS	HUVEC	blood vessel
31	chr1:151042600-151043200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:151042600-151043400	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr1:151042600-151043600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:151042600-151043600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:151042600-151043600	ZNF genes & repeats	Fetal Brain Male	brain
36	chr1:151042600-151043800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:151042600-151043800	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:151042600-151043800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:151042600-151043800	Active TSS	Stomach Mucosa	stomach
40	chr1:151042600-151043800	Active TSS	Stomach Smooth Muscle	stomach
41	chr1:151042600-151044000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr1:151042600-151044000	Active TSS	H1 Cell Line	embryonic stem cell
43	chr1:151042600-151044000	Active TSS	H9 Cell Line	embryonic stem cell
44	chr1:151042600-151044000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:151042600-151044000	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr1:151042600-151044000	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr1:151042600-151044000	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr1:151042600-151044000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:151042600-151044000	Active TSS	Primary T helper naive cells from peripheral blood	blood
50	chr1:151042600-151044000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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