Variant report

Variant	rs10888439
Chromosome Location	chr1:151812032-151812033
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	TAF1	chr1:151811938-151812802	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:151811902-151812864	MCF-7	breast:	n/a	n/a
3	TCF12	chr1:151812021-151812390	H1-hESC	embryonic stem cell:	n/a	chr1:151812164-151812171
4	TAF1	chr1:151811943-151812624	ECC-1	luminal epithelium:	n/a	n/a
5	EBF1	chr1:151811756-151812110	GM12878	blood:	n/a	chr1:151811998-151812009 chr1:151811997-151812010 chr1:151811906-151811919
6	POLR2A	chr1:151811909-151812865	MCF-7	breast:	n/a	n/a
7	ZEB1	chr1:151811884-151812396	GM12878	blood:	n/a	chr1:151812161-151812170
8	MAX	chr1:151811973-151812532	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr1:151811648-151812942	MCF-7	breast:	n/a	n/a
10	WRNIP1	chr1:151812026-151812371	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:151811949-151812752	PANC-1	pancreas:	n/a	n/a
12	CTCF	chr1:151812000-151812150	NHEK	skin:	n/a	n/a
13	JUND	chr1:151811998-151812783	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:151811951-151812746	GM12878	blood:	n/a	n/a
15	RAD21	chr1:151811871-151812384	H1-hESC	embryonic stem cell:	n/a	chr1:151812102-151812114 chr1:151812155-151812165 chr1:151812079-151812093
16	POLR2A	chr1:151811938-151812857	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr1:151811862-151812863	GM12878	blood:	n/a	n/a
18	MAX	chr1:151811972-151812781	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr1:151810965-151813837	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:151811872-151812737	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAZ	chr1:151811959-151812941	GM12878	blood:	n/a	n/a
22	MAX	chr1:151812003-151812733	ECC-1	luminal epithelium:	n/a	n/a
23	MAX	chr1:151811870-151813355	MCF-7	breast:	n/a	n/a
24	MYC	chr1:151811856-151812616	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:151811884-151812892	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:151812014-151812696	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:151811891-151813029	H1-hESC	embryonic stem cell:	n/a	n/a
28	RAD21	chr1:151811972-151812642	H1-hESC	embryonic stem cell:	n/a	chr1:151812102-151812114 chr1:151812589-151812599 chr1:151812530-151812543 chr1:151812155-151812165 chr1:151812079-151812093
29	ELF1	chr1:151811840-151812798	GM12878	blood:	n/a	n/a
30	MAX	chr1:151811910-151812694	H1-hESC	embryonic stem cell:	n/a	n/a
31	HDAC2	chr1:151811487-151813549	MCF-7	breast:	n/a	n/a
32	HDAC2	chr1:151811902-151813102	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:151811876-151812898	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:151811919-151812724	ProgFib	skin:	n/a	n/a
35	TBP	chr1:151811867-151812776	H1-hESC	embryonic stem cell:	n/a	n/a
36	TBP	chr1:151811914-151812628	GM12878	blood:	n/a	n/a
37	EBF1	chr1:151811736-151812086	GM12878	blood:	n/a	chr1:151811998-151812009 chr1:151811997-151812010 chr1:151811906-151811919
38	TCF12	chr1:151811920-151812656	ECC-1	luminal epithelium:	n/a	chr1:151812164-151812171
39	CTCF	chr1:151811980-151812130	MCF-7	breast:	n/a	n/a
40	CHD2	chr1:151811963-151812513	H1-hESC	embryonic stem cell:	n/a	n/a
41	PML	chr1:151811887-151813391	MCF-7	breast:	n/a	chr1:151812602-151812610
42	ZBTB7A	chr1:151811800-151812706	ECC-1	luminal epithelium:	n/a	chr1:151811997-151812004
43	SPI1	chr1:151811861-151812274	GM12878	blood:	n/a	n/a
44	NR2F2	chr1:151811722-151813271	MCF-7	breast:	n/a	n/a
45	CTCF	chr1:151812020-151812170	GM12866	blood:	n/a	n/a
46	MAX	chr1:151811864-151812865	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:151811969-151812627	GM19099	blood:	n/a	n/a
48	CTCF	chr1:151812000-151812150	GM06990	blood:	n/a	n/a
49	SP1	chr1:151811883-151812503	H1-hESC	embryonic stem cell:	n/a	chr1:151812230-151812241 chr1:151811949-151811958 chr1:151812297-151812309 chr1:151811950-151811959 chr1:151812299-151812308 chr1:151812297-151812309
50	PML	chr1:151811980-151812956	MCF-7	breast:	n/a	chr1:151812602-151812610

No.	Distal block	Cell Line	Cell type
1	chr1:151510584..151515702-chr1:151808389..151812312,7	MCF-7	breast:
2	chr1:151811113..151814780-chr1:151962857..151966577,5	MCF-7	breast:
3	chr1:151481758..151484470-chr1:151811083..151813836,2	MCF-7	breast:
4	chr1:151797661..151799547-chr1:151812000..151814982,2	MCF-7	breast:
5	chr1:151509575..151514119-chr1:151809649..151812293,5	MCF-7	breast:
6	chr1:151517981..151521165-chr1:151811031..151814404,3	MCF-7	breast:
7	chr1:151804539..151806807-chr1:151808292..151812161,4	K562	blood:
8	chr1:151811289..151813679-chr17:43235374..43237810,2	MCF-7	breast:
9	chr1:151734307..151737224-chr1:151809345..151813879,7	MCF-7	breast:
10	chr1:151542468..151544552-chr1:151811303..151812825,2	MCF-7	breast:
11	chr1:151506418..151509266-chr1:151811121..151813998,3	MCF-7	breast:
12	chr1:151717253..151722089-chr1:151808382..151812448,4	MCF-7	breast:
13	chr1:151810783..151812535-chr1:151860499..151863108,2	MCF-7	breast:
14	chr1:151804012..151806616-chr1:151810661..151813276,2	K562	blood:
15	chr1:151810931..151813859-chr1:151881520..151883452,3	MCF-7	breast:
16	chr1:151371973..151373501-chr1:151810861..151813533,2	MCF-7	breast:
17	chr1:151811099..151812634-chr7:103621578..103623542,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234614	TF binding region
ENSG00000207606	Chromatin interaction
ENSG00000159445	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000206980	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000143375	Chromatin interaction
ENSG00000224505	Chromatin interaction
ENSG00000197747	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10788810	0.81[ASN][1000 genomes]
rs11204899	0.87[EUR][1000 genomes]
rs11204900	0.83[EUR][1000 genomes]
rs11204901	0.85[EUR][1000 genomes]
rs12122596	0.87[ASN][1000 genomes]
rs12140021	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7536659	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7544269	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7551686	0.87[ASN][1000 genomes]
rs7551806	0.86[ASN][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	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv1804657	chr1:151784152-151825756	Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1008033	chr1:151785029-151843154	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv3360539	chr1:151809753-151812301	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151809600-151812800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:151810000-151818800	Weak transcription	A549	lung
3	chr1:151810200-151812400	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
4	chr1:151810200-151812600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
5	chr1:151810200-151812800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:151810400-151812400	Weak transcription	Hela-S3	cervix
7	chr1:151810400-151812600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr1:151810400-151812600	Flanking Active TSS	Right Ventricle	heart
9	chr1:151810400-151812800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:151810400-151812800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:151810400-151812800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
12	chr1:151810400-151812800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:151810400-151812800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:151810400-151812800	Flanking Bivalent TSS/Enh	Thymus	Thymus
15	chr1:151810400-151812800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
16	chr1:151810400-151813000	Active TSS	Brain Substantia Nigra	brain
17	chr1:151810600-151812600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:151810600-151813000	Active TSS	H9 Cell Line	embryonic stem cell
19	chr1:151810600-151813000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:151810800-151812400	Active TSS	Esophagus	oesophagus
21	chr1:151810800-151813000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:151810800-151813200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
23	chr1:151810800-151813200	Flanking Active TSS	HMEC	breast
24	chr1:151811000-151812400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:151811000-151812400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:151811000-151812400	Enhancers	Lung	lung
27	chr1:151811000-151812400	Enhancers	Small Intestine	intestine
28	chr1:151811000-151812600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
29	chr1:151811200-151812200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr1:151811200-151812400	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
31	chr1:151811200-151812600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
32	chr1:151811200-151812800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr1:151811200-151812800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr1:151811200-151813000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:151811200-151813000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr1:151811200-151813200	Bivalent Enhancer	Fetal Lung	lung
37	chr1:151811400-151812200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
38	chr1:151811400-151812200	Flanking Active TSS	Brain Anterior Caudate	brain
39	chr1:151811400-151812200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
40	chr1:151811400-151812400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:151811400-151812400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:151811400-151812400	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr1:151811400-151812400	Bivalent/Poised TSS	Psoas Muscle	Psoas
44	chr1:151811400-151812400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr1:151811400-151812600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
46	chr1:151811400-151812600	Bivalent Enhancer	Fetal Heart	heart
47	chr1:151811400-151812600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
48	chr1:151811400-151812800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:151811400-151812800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
50	chr1:151811400-151813000	Flanking Active TSS	Duodenum Mucosa	Duodenum

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