Variant report

Variant	rs16832550
Chromosome Location	chr1:45974776-45974777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:98)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:98 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr1:45973568-45975082	GM12878	blood:	n/a	n/a
2	FOSL2	chr1:45973875-45974962	HepG2	liver:	n/a	n/a
3	JUND	chr1:45972871-45975112	A549	lung:	n/a	chr1:45973476-45973490
4	HEY1	chr1:45974760-45975050	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:45972866-45975153	HCT-116	colon:	n/a	n/a
6	JUND	chr1:45973695-45975056	HCT-116	colon:	n/a	n/a
7	POLR2A	chr1:45973385-45974853	U87	brain:	n/a	n/a
8	POLR2A	chr1:45973845-45974852	GM12892	blood:	n/a	n/a
9	POLR2A	chr1:45974091-45975002	K562	blood:	n/a	n/a
10	POLR2A	chr1:45973000-45974988	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:45972808-45975056	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:45973723-45974934	GM12878	blood:	n/a	n/a
13	CCNT2	chr1:45974672-45974879	K562	blood:	n/a	n/a
14	POLR2A	chr1:45974623-45974912	IMR90	lung:	n/a	n/a
15	POLR2A	chr1:45972877-45974916	A549	lung:	n/a	n/a
16	POLR2A	chr1:45972838-45975218	PANC-1	pancreas:	n/a	n/a
17	JUND	chr1:45972476-45975008	A549	lung:	n/a	chr1:45973476-45973490
18	POLR2A	chr1:45973274-45974958	U87	brain:	n/a	n/a
19	PML	chr1:45973923-45975170	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:45972867-45979125	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr1:45973966-45974899	K562	blood:	n/a	n/a
22	POLR2A	chr1:45972932-45976748	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:45974473-45974891	GM18951	blood:	n/a	n/a
24	POLR2A	chr1:45973854-45974965	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr1:45972796-45975088	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr1:45973724-45974879	A549	lung:	n/a	n/a
27	POLR2A	chr1:45973197-45975216	GM12891	blood:	n/a	n/a
28	POLR2A	chr1:45972821-45975013	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr1:45973208-45975384	K562	blood:	n/a	n/a
30	POLR2A	chr1:45973399-45974958	U87	brain:	n/a	n/a
31	NFATC1	chr1:45973819-45974829	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:45973915-45974860	GM19193	blood:	n/a	n/a
33	POLR2A	chr1:45972667-45975035	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:45972687-45978691	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr1:45973921-45975042	K562	blood:	n/a	n/a
36	POLR2A	chr1:45972840-45975205	K562	blood:	n/a	n/a
37	POLR2A	chr1:45973577-45974973	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:45973017-45975225	GM12892	blood:	n/a	n/a
39	ATF3	chr1:45973345-45974842	A549	lung:	n/a	n/a
40	POLR2A	chr1:45973292-45977716	HepG2	liver:	n/a	n/a
41	SIX5	chr1:45974174-45974903	A549	lung:	n/a	n/a
42	TCF12	chr1:45972856-45974890	A549	lung:	n/a	chr1:45973677-45973684
43	POLR2A	chr1:45973730-45974897	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr1:45972974-45979094	K562	blood:	n/a	n/a
45	POLR2A	chr1:45973506-45975087	HCT-116	colon:	n/a	n/a
46	POLR2A	chr1:45973660-45974869	GM12891	blood:	n/a	n/a
47	POLR2A	chr1:45972877-45977732	HepG2	liver:	n/a	n/a
48	POLR2A	chr1:45972966-45975090	HepG2	liver:	n/a	n/a
49	POLR2A	chr1:45973928-45974914	K562	blood:	n/a	n/a
50	POLR2A	chr1:45973185-45976753	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45973068..45975148-chr1:46049390..46051110,2	MCF-7	breast:
2	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
3	chr1:45973182..45975128-chr1:45984664..45989019,3	MCF-7	breast:
4	chr1:45965671..45969478-chr1:45972057..45975317,5	MCF-7	breast:
5	chr1:45972145..45974948-chr1:46590172..46592785,2	K562	blood:
6	chr1:45805983..45807549-chr1:45973532..45975768,2	K562	blood:

No data

Variant related genes	Relation type
MMACHC	TF binding region
ENSG00000132781	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000132763	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs11211125	1.00[EUR][1000 genomes]
rs11211127	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211144	1.00[AMR][1000 genomes]
rs11211148	1.00[AMR][1000 genomes]
rs11211153	1.00[AMR][1000 genomes]
rs11211154	1.00[AMR][1000 genomes]
rs11211155	1.00[AMR][1000 genomes]
rs11211156	1.00[AMR][1000 genomes]
rs11211167	1.00[AMR][1000 genomes]
rs12057167	1.00[AMR][1000 genomes]
rs12060056	1.00[AMR][1000 genomes]
rs12061890	1.00[AMR][1000 genomes]
rs12063380	1.00[AMR][1000 genomes]
rs12064908	1.00[AMR][1000 genomes]
rs12065695	1.00[EUR][1000 genomes]
rs12066809	1.00[EUR][1000 genomes]
rs12067882	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12070146	1.00[AMR][1000 genomes]
rs12070177	1.00[AMR][1000 genomes]
rs12070890	1.00[EUR][1000 genomes]
rs12073045	1.00[AMR][1000 genomes]
rs12073047	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073132	1.00[AMR][1000 genomes]
rs12077112	1.00[AMR][1000 genomes]
rs12080482	1.00[AMR][1000 genomes]
rs12081121	1.00[AMR][1000 genomes]
rs12082672	1.00[AMR][1000 genomes]
rs12083690	1.00[EUR][1000 genomes]
rs12085372	1.00[AMR][1000 genomes]
rs12086880	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088810	1.00[AMR][1000 genomes]
rs12091335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091360	1.00[AMR][1000 genomes]
rs12093444	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12094011	1.00[AMR][1000 genomes]
rs12097914	1.00[AMR][1000 genomes]
rs12565230	1.00[EUR][1000 genomes]
rs16832540	1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832545	1.00[EUR][1000 genomes]
rs16832553	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16832557	1.00[ASW][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16832559	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1691225	1.00[AMR][1000 genomes]
rs1691226	1.00[AMR][1000 genomes]
rs1691227	1.00[AMR][1000 genomes]
rs1762087	1.00[AMR][1000 genomes]
rs1855621	1.00[EUR][1000 genomes]
rs2782489	1.00[AMR][1000 genomes]
rs28532613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28607905	1.00[AMR][1000 genomes]
rs2934860	1.00[EUR][1000 genomes]
rs2934861	1.00[EUR][1000 genomes]
rs2934863	1.00[EUR][1000 genomes]
rs2934864	1.00[EUR][1000 genomes]
rs2991967	1.00[EUR][1000 genomes]
rs2991969	1.00[EUR][1000 genomes]
rs2991984	1.00[EUR][1000 genomes]
rs2993256	1.00[EUR][1000 genomes]
rs2993260	1.00[EUR][1000 genomes]
rs2993261	1.00[EUR][1000 genomes]
rs3014222	1.00[EUR][1000 genomes]
rs3014223	1.00[EUR][1000 genomes]
rs3014224	1.00[EUR][1000 genomes]
rs3014226	1.00[EUR][1000 genomes]
rs35067820	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35103566	1.00[EUR][1000 genomes]
rs35808563	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36053912	1.00[EUR][1000 genomes]
rs486346	1.00[AMR][1000 genomes]
rs505175	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs506094	1.00[AMR][1000 genomes]
rs525706	1.00[AMR][1000 genomes]
rs57910611	1.00[EUR][1000 genomes]
rs59050426	1.00[EUR][1000 genomes]
rs60347972	1.00[EUR][1000 genomes]
rs60660559	1.00[EUR][1000 genomes]
rs622296	1.00[AMR][1000 genomes]
rs635446	1.00[AMR][1000 genomes]
rs665014	1.00[AMR][1000 genomes]
rs6664588	1.00[EUR][1000 genomes]
rs6671347	1.00[EUR][1000 genomes]
rs6677135	1.00[EUR][1000 genomes]
rs668289	1.00[AMR][1000 genomes]
rs669417	1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs6699702	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs680267	1.00[AMR][1000 genomes]
rs72896187	1.00[EUR][1000 genomes]
rs72898313	1.00[EUR][1000 genomes]
rs72898315	1.00[EUR][1000 genomes]
rs72898320	1.00[EUR][1000 genomes]
rs72898323	1.00[EUR][1000 genomes]
rs72900311	1.00[EUR][1000 genomes]
rs7412911	1.00[EUR][1000 genomes]
rs7536559	1.00[EUR][1000 genomes]
rs7550744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9429080	1.00[EUR][1000 genomes]
rs9429083	1.00[EUR][1000 genomes]
rs9429164	1.00[EUR][1000 genomes]
rs9429165	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 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	chr1:45966400-45975600	Weak transcription	HSMMtube	muscle
2	chr1:45966400-45975800	Weak transcription	Aorta	Aorta
3	chr1:45966600-45984600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:45966800-45975800	Weak transcription	HSMM	muscle
5	chr1:45966800-45975800	Weak transcription	NHDF-Ad	bronchial
6	chr1:45966800-45976000	Weak transcription	Fetal Brain Male	brain
7	chr1:45966800-45976000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:45966800-45980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:45966800-45984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:45967000-45975400	Weak transcription	NH-A	brain
11	chr1:45967000-45975600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:45967000-45975800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:45967000-45977200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:45967200-45975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:45967200-45975400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:45967200-45975400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:45967200-45975600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:45967200-45975600	Weak transcription	Psoas Muscle	Psoas
19	chr1:45967200-45975800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:45967200-45976200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:45967200-45976200	Weak transcription	Fetal Lung	lung
22	chr1:45967400-45975600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:45967400-45975800	Weak transcription	Stomach Mucosa	stomach
24	chr1:45971600-45985000	Strong transcription	Fetal Stomach	stomach
25	chr1:45971800-45980400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:45971800-45982000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:45972800-45975000	Genic enhancers	HepG2	liver
28	chr1:45972800-45978200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:45972800-45978400	Strong transcription	Fetal Intestine Small	intestine
30	chr1:45972800-45980400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:45972800-45982200	Strong transcription	K562	blood
32	chr1:45972800-45982400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:45972800-45984400	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:45972800-45984400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:45972800-45984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:45972800-45984600	Strong transcription	Fetal Thymus	thymus
37	chr1:45973000-45974800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:45973000-45974800	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr1:45973000-45975000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr1:45973000-45976800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr1:45973000-45981800	Strong transcription	Dnd41	blood
42	chr1:45973000-45983000	Strong transcription	Fetal Brain Female	brain
43	chr1:45973000-45983200	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr1:45973000-45983200	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr1:45973000-45983400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:45973000-45983800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:45973000-45983800	Strong transcription	Spleen	Spleen
48	chr1:45973000-45984000	Strong transcription	Primary T cells from cord blood	blood
49	chr1:45973000-45984000	Strong transcription	Fetal Muscle Trunk	muscle
50	chr1:45973000-45984000	Strong transcription	Fetal Muscle Leg	muscle

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