Variant report

Variant	rs11571525
Chromosome Location	chr1:212784969-212784970
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	chr1:212778466-212788906	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:212778349-212787926	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:212780956-212787804	HepG2	liver:	n/a	n/a
4	MAZ	chr1:212780603-212785387	IMR90	lung:	n/a	chr1:212781008-212781017 chr1:212781961-212781971 chr1:212781900-212781909 chr1:212781860-212781870 chr1:212782384-212782394 chr1:212782770-212782779 chr1:212782716-212782726 chr1:212781677-212781687 chr1:212781009-212781016
5	POLR2A	chr1:212780146-212787893	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:212784063-212785234	K562	blood:	n/a	n/a
7	POLR2A	chr1:212779324-212788938	Hela-S3	cervix:	n/a	n/a
8	CHD1	chr1:212779286-212788865	IMR90	lung:	n/a	chr1:212783477-212783487 chr1:212782811-212782821
9	POLR2A	chr1:212779999-212787934	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:212780020-212789160	H1-hESC	embryonic stem cell:	n/a	n/a
11	PRDM1	chr1:212784958-212785324	Hela-S3	cervix:	n/a	chr1:212785126-212785139 chr1:212785125-212785139 chr1:212785126-212785135 chr1:212785124-212785139 chr1:212785042-212785056
12	POLR2A	chr1:212783571-212785066	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:212779987-212787925	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:212780258-212787842	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:212784826-212785075	GM12878	blood:	n/a	n/a
16	HCFC1	chr1:212778936-212785331	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:212781346-212789662	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:212780144-212798001	IMR90	lung:	n/a	n/a
19	POLR2A	chr1:212781260-212785310	HCT-116	colon:	n/a	n/a
20	STAT3	chr1:212784801-212784995	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:212783908-212785107	GM12892	blood:	n/a	n/a
22	POLR2A	chr1:212783529-212785027	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:212784490-212784989	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:212784442-212784972	K562	blood:	n/a	n/a
25	MAFK	chr1:212784147-212785071	Hela-S3	cervix:	n/a	chr1:212784527-212784544
26	POLR2A	chr1:212783591-212784999	GM12892	blood:	n/a	n/a
27	POLR2A	chr1:212781301-212786675	K562	blood:	n/a	n/a
28	POLR2A	chr1:212782514-212798502	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:212783105..212785430-chr1:212837699..212841392,3	K562	blood:
2	chr1:212781960..212786594-chr1:212837699..212841392,5	K562	blood:
3	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
4	chr1:206722322..206724885-chr1:212783565..212785335,2	K562	blood:
5	chr1:212780951..212783971-chr1:212784548..212788701,9	MCF-7	breast:
6	chr1:212663057..212665371-chr1:212783064..212784989,2	MCF-7	breast:
7	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
8	chr1:212782866..212786640-chr1:213033437..213035689,3	K562	blood:
9	chr1:212757622..212760525-chr1:212782938..212786517,3	K562	blood:
10	chr1:212712241..212714137-chr1:212784111..212786006,2	K562	blood:
11	chr1:212783925..212785480-chr1:213147675..213150119,2	K562	blood:
12	chr1:212783045..212785290-chr1:213295764..213298045,2	K562	blood:
13	chr1:212779956..212785175-chr1:212870276..212874748,7	K562	blood:
14	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:
15	chr1:212670285..212672313-chr1:212782929..212785774,2	K562	blood:
16	chr1:212779632..212786722-chr1:212965265..212968763,9	K562	blood:
17	chr1:212779632..212786722-chr1:212963640..212968604,10	K562	blood:

Variant related genes	Relation type
ATF3	TF binding region
ENSG00000203705	Chromatin interaction
ENSG00000237980	Chromatin interaction
ENSG00000123685	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction
ENSG00000260805	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000117697	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10465692	1.00[AMR][1000 genomes]
rs11571523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11571531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55727989	1.00[AMR][1000 genomes]
rs56056407	1.00[AMR][1000 genomes]
rs56059979	1.00[AMR][1000 genomes]
rs56909493	1.00[AMR][1000 genomes]
rs57517430	1.00[AMR][1000 genomes]
rs58964221	1.00[AMR][1000 genomes]
rs60404556	1.00[AMR][1000 genomes]
rs61460239	1.00[AMR][1000 genomes]
rs74138137	1.00[AMR][1000 genomes]
rs74138138	1.00[AMR][1000 genomes]
rs74138139	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
5	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
6	nsv428588	chr1:212705588-212862875	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212779800-212785000	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:212783200-212785000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr1:212783200-212785200	Flanking Active TSS	GM12878-XiMat	blood
4	chr1:212783200-212785800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:212783400-212785200	Enhancers	Small Intestine	intestine
6	chr1:212783400-212790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:212783400-212791600	Weak transcription	Ovary	ovary
8	chr1:212783600-212785000	Enhancers	K562	blood
9	chr1:212783600-212788200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:212783600-212792000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:212783800-212785000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:212783800-212785000	Enhancers	Fetal Heart	heart
13	chr1:212783800-212785000	Flanking Active TSS	Placenta	Placenta
14	chr1:212784000-212785000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr1:212784000-212785000	Enhancers	Brain Substantia Nigra	brain
16	chr1:212784000-212785000	Enhancers	Lung	lung
17	chr1:212784000-212785000	Flanking Active TSS	NHDF-Ad	bronchial
18	chr1:212784000-212785000	Flanking Active TSS	Osteobl	bone
19	chr1:212784000-212787000	Weak transcription	Spleen	Spleen
20	chr1:212784000-212787800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:212784000-212792000	Weak transcription	Esophagus	oesophagus
22	chr1:212784000-212794200	Weak transcription	HUVEC	blood vessel
23	chr1:212784200-212785000	Enhancers	Right Atrium	heart
24	chr1:212784200-212785000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
25	chr1:212784200-212785200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:212784200-212785200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:212784200-212785400	Enhancers	HepG2	liver
28	chr1:212784200-212785800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:212784200-212786200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:212784200-212787200	Enhancers	H9 Cell Line	embryonic stem cell
31	chr1:212784200-212787200	Weak transcription	Gastric	stomach
32	chr1:212784200-212787400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:212784200-212788400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:212784200-212788600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:212784200-212788600	Weak transcription	Fetal Intestine Large	intestine
36	chr1:212784200-212789200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:212784200-212790400	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr1:212784200-212796800	Weak transcription	Stomach Mucosa	stomach
39	chr1:212784400-212785000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:212784400-212785000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:212784400-212785000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:212784400-212785000	Enhancers	Placenta Amnion	Placenta Amnion
43	chr1:212784400-212785000	Enhancers	Psoas Muscle	Psoas
44	chr1:212784400-212785000	Active TSS	Stomach Smooth Muscle	stomach
45	chr1:212784400-212786400	Enhancers	Aorta	Aorta
46	chr1:212784400-212786600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
47	chr1:212784400-212786800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:212784400-212787000	Weak transcription	Fetal Intestine Small	intestine
49	chr1:212784400-212787800	Enhancers	Brain Hippocampus Middle	brain
50	chr1:212784400-212788000	Weak transcription	Fetal Stomach	stomach

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