Variant report

Variant	rs10880959
Chromosome Location	chr12:46761127-46761128
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	chr12:46750625-46766899	K562	blood:	n/a	n/a
2	POLR2A	chr12:46760947-46761192	K562	blood:	n/a	n/a
3	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:46760562-46762281	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:46760573-46767926	Hela-S3	cervix:	n/a	n/a
7	E2F4	chr12:46760695-46761452	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr12:46760857-46764495	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
12	SIN3AK20	chr12:46760999-46761820	HCT-116	colon:	n/a	n/a
13	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
14	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509
15	POLR2A	chr12:46761022-46761791	GM12892	blood:	n/a	n/a
16	MYC	chr12:46760735-46761146	MCF10A-Er-Src	breast:	n/a	chr12:46760770-46760779 chr12:46760769-46760780 chr12:46760765-46760784
17	POLR2A	chr12:46754387-46768013	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr12:46761019-46762624	GM12892	blood:	n/a	n/a
19	POLR2A	chr12:46754499-46767455	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr12:46760417-46762116	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr12:46761065-46761881	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:46757607-46767342	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr12:46760364-46767099	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr12:46750487-46766675	A549	lung:	n/a	n/a
25	POLR2A	chr12:46758684-46767978	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr12:46761002-46763912	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:46758139-46766914	MCF-7	breast:	n/a	n/a
28	POLR2A	chr12:46761126-46761272	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:46754358-46767861	HepG2	liver:	n/a	n/a
30	POLR2A	chr12:46755082-46767953	HCT-116	colon:	n/a	n/a
31	NFIC	chr12:46760670-46761460	HepG2	liver:	n/a	chr12:46761293-46761310
32	POLR2A	chr12:46758424-46767361	MCF10A-Er-Src	breast:	n/a	n/a
33	POLR2A	chr12:46750385-46767599	IMR90	lung:	n/a	n/a
34	POLR2A	chr12:46760980-46762251	GM12891	blood:	n/a	n/a
35	HEY1	chr12:46750801-46768173	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
36	POLR2A	chr12:46761038-46764152	ProgFib	skin:	n/a	n/a
37	MBD4	chr12:46750663-46767066	HepG2	liver:	n/a	n/a
38	POLR2A	chr12:46760588-46763976	K562	blood:	n/a	n/a
39	POLR2A	chr12:46760525-46761334	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr12:46761095-46761828	GM12891	blood:	n/a	n/a
41	POLR2A	chr12:46760978-46764013	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:46754307-46767479	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr12:46761024-46761673	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr12:46750204-46767088	U87	brain:	n/a	n/a
45	POLR2A	chr12:46761091-46761714	GM12892	blood:	n/a	n/a
46	POLR2A	chr12:46758610-46767931	HUVEC	blood vessel:	n/a	n/a
47	POLR2A	chr12:46759062-46767808	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr12:46760481-46767380	U87	brain:	n/a	n/a
49	POLR2A	chr12:46760577-46762330	K562	blood:	n/a	n/a
50	POLR2A	chr12:46760534-46763768	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
2	chr12:46660616..46664726-chr12:46759249..46761419,3	MCF-7	breast:
3	chr12:46661733..46663238-chr12:46759583..46762194,2	K562	blood:
4	chr12:46760893..46761645-chr2:113341924..113342581,2	Hela-S3	cervix:
5	chr1:212731662..212732424-chr12:46760558..46761178,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000258096	TF binding region
SLC38A2	TF binding region
ENSG00000111371	Chromatin interaction
ENSG00000125611	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10467213	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1079780	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880947	0.81[EUR][1000 genomes]
rs10880953	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10880960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10880961	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11183441	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12298619	0.81[EUR][1000 genomes]
rs12310125	0.80[EUR][1000 genomes]
rs12311507	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12317787	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12580583	0.81[EUR][1000 genomes]
rs12816358	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12816413	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1471223	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1492892	0.80[EUR][1000 genomes]
rs1492894	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2018424	0.80[EUR][1000 genomes]
rs2169030	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2307061	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2408504	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2408505	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2408506	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2408507	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2408508	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2897968	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34119192	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35497251	0.80[EUR][1000 genomes]
rs3782904	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4238102	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4438106	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4547171	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4586238	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768111	0.81[EUR][1000 genomes]
rs4768115	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768116	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768695	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768696	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4768698	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59919892	0.80[EUR][1000 genomes]
rs6582625	0.81[EUR][1000 genomes]
rs7132228	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7134855	0.81[EUR][1000 genomes]
rs7314069	0.81[EUR][1000 genomes]
rs7315493	0.81[EUR][1000 genomes]
rs7316127	0.81[EUR][1000 genomes]
rs7953659	0.80[EUR][1000 genomes]
rs7958774	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7960147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961994	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7965629	0.81[EUR][1000 genomes]
rs7966288	0.81[EUR][1000 genomes]
rs7967669	0.80[EUR][1000 genomes]
rs7968173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7968283	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7974529	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7976362	0.81[EUR][1000 genomes]
rs7979418	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7979514	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7980775	0.81[EUR][1000 genomes]
rs898242	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs956910	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9668077	0.88[AMR][1000 genomes]
rs9669051	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9669381	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9795971	0.88[AMR][1000 genomes];0.84[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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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 target site	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 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	chr12:46737600-46761200	Weak transcription	Gastric	stomach
2	chr12:46748800-46764200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:46750400-46761200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:46751600-46761200	Strong transcription	Fetal Brain Female	brain
5	chr12:46752200-46761200	Strong transcription	Placenta	Placenta
6	chr12:46752400-46761400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr12:46752400-46761600	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:46752400-46761600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:46752400-46761800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr12:46752400-46764200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:46752600-46761200	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr12:46752600-46761200	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:46752600-46761400	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr12:46752600-46761600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:46752600-46762400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:46752600-46763000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:46752600-46763600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:46752600-46764200	Strong transcription	Fetal Muscle Trunk	muscle
19	chr12:46752800-46761200	Strong transcription	Left Ventricle	heart
20	chr12:46752800-46761600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr12:46752800-46762000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:46753000-46762600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:46753400-46761200	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr12:46753400-46761800	Strong transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:46753400-46762400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr12:46753400-46764200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:46753600-46761200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr12:46753600-46761600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:46753600-46765200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:46754000-46761200	Genic enhancers	Primary T cells from cord blood	blood
31	chr12:46754000-46761200	Weak transcription	Esophagus	oesophagus
32	chr12:46754000-46765800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:46754600-46762600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr12:46754600-46765000	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr12:46754800-46762600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:46755800-46761200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:46755800-46761200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr12:46756200-46762200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:46756600-46761200	Active TSS	Right Atrium	heart
41	chr12:46756600-46761600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:46756600-46762000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:46756600-46765200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:46756800-46763000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr12:46756800-46766000	Transcr. at gene 5' and 3'	NHLF	lung
46	chr12:46757000-46763600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr12:46757400-46761200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:46757400-46761200	Genic enhancers	Brain Hippocampus Middle	brain
49	chr12:46757400-46762200	Genic enhancers	Placenta Amnion	Placenta Amnion
50	chr12:46757400-46766000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--

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