Variant report

Variant	rs11571538
Chromosome Location	chr1:212787092-212787093
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:48)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:48 , 50 per page) page: 1

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	chr1:212786845-212787849	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:212786825-212787239	U87	brain:	n/a	n/a
4	POLR2A	chr1:212778349-212787926	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:212780956-212787804	HepG2	liver:	n/a	n/a
6	CTCF	chr1:212787000-212787150	RPTEC	kidney:	n/a	n/a
7	CTCF	chr1:212787000-212787150	WI-38	lung:	n/a	n/a
8	CTCF	chr1:212787034-212787148	Fibrobl	skin:	n/a	n/a
9	POLR2A	chr1:212780146-212787893	GM12878	blood:	n/a	n/a
10	CTCF	chr1:212787020-212787170	AG04449	skin:	n/a	n/a
11	CTCF	chr1:212787080-212787230	HMF	breast:	n/a	n/a
12	CTCF	chr1:212786980-212787130	HMEC	breast:	n/a	n/a
13	POLR2A	chr1:212779324-212788938	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr1:212787060-212787210	BE2_C	brain:	n/a	n/a
15	CTCF	chr1:212787020-212787170	HBMEC	blood vessel:	n/a	n/a
16	CHD1	chr1:212779286-212788865	IMR90	lung:	n/a	chr1:212783477-212783487 chr1:212782811-212782821
17	CTCF	chr1:212787060-212787132	ProgFib	skin:	n/a	n/a
18	POLR2A	chr1:212786782-212787895	K562	blood:	n/a	n/a
19	CTCF	chr1:212787020-212787170	HPF	lung:	n/a	n/a
20	POLR2A	chr1:212779999-212787934	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:212780020-212789160	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr1:212787080-212787230	AG09309	skin:	n/a	n/a
23	CTCF	chr1:212786980-212787130	HPAF	blood vessel:	n/a	n/a
24	POLR2A	chr1:212786741-212787870	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:212786949-212787661	GM12891	blood:	n/a	n/a
26	POLR2A	chr1:212779987-212787925	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr1:212786918-212787816	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr1:212786833-212787775	H1-hESC	embryonic stem cell:	n/a	n/a
29	EBF1	chr1:212786959-212787254	GM12878	blood:	n/a	chr1:212787077-212787088
30	POLR2A	chr1:212785209-212787245	K562	blood:	n/a	n/a
31	POLR2A	chr1:212780258-212787842	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr1:212787092-212787143	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:212781346-212789662	HepG2	liver:	n/a	n/a
34	POLR2A	chr1:212780144-212798001	IMR90	lung:	n/a	n/a
35	CTCF	chr1:212787040-212787190	HMF	breast:	n/a	n/a
36	EBF1	chr1:212786860-212787277	GM12878	blood:	n/a	chr1:212787077-212787088
37	POLR2A	chr1:212786792-212787297	U87	brain:	n/a	n/a
38	POLR2A	chr1:212786283-212787306	K562	blood:	n/a	n/a
39	CTCF	chr1:212787000-212787150	AoAF	blood vessel:	n/a	n/a
40	POLR2A	chr1:212786918-212787222	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr1:212787002-212787906	PFSK-1	brain:	n/a	n/a
42	POLR2A	chr1:212786774-212787870	GM12892	blood:	n/a	n/a
43	POLR2A	chr1:212786411-212787212	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:212786770-212787836	Hela-S3	cervix:	n/a	n/a
45	EBF1	chr1:212786888-212787252	GM12878	blood:	n/a	chr1:212787077-212787088
46	CTCF	chr1:212786960-212787110	AG10803	skin:	n/a	n/a
47	CTCF	chr1:212786960-212787110	HCFaa	heart:	n/a	n/a
48	POLR2A	chr1:212782514-212798502	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212785851..212789357-chr1:212837777..212840991,5	K562	blood:
2	chr1:212780951..212783971-chr1:212784548..212788701,9	MCF-7	breast:
3	chr1:212729491..212744666-chr1:212778733..212791648,68	K562	blood:
4	chr1:212729172..212744062-chr1:212776412..212791648,77	K562	blood:

No data

Variant related genes	Relation type
ATF3	TF binding region
ENSG00000260805	Chromatin interaction
ENSG00000237980	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11571532	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11571536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11571552	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17019442	1.00[CHB][hapmap];0.88[MEX][hapmap];1.00[ASN][1000 genomes]
rs35777725	1.00[ASN][1000 genomes]
rs3890801	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs55854080	1.00[ASN][1000 genomes]
rs6540751	1.00[ASN][1000 genomes]
rs6656504	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6666492	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes]
rs6670396	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6682816	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72756370	1.00[ASN][1000 genomes]
rs72756371	1.00[ASN][1000 genomes]
rs74138596	1.00[ASN][1000 genomes]
rs74138599	1.00[ASN][1000 genomes]
rs74138600	1.00[ASN][1000 genomes]
rs74138601	1.00[ASN][1000 genomes]
rs7551520	1.00[ASN][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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212783400-212790400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:212783400-212791600	Weak transcription	Ovary	ovary
3	chr1:212783600-212788200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:212783600-212792000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:212784000-212787800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:212784000-212792000	Weak transcription	Esophagus	oesophagus
7	chr1:212784000-212794200	Weak transcription	HUVEC	blood vessel
8	chr1:212784200-212787200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr1:212784200-212787200	Weak transcription	Gastric	stomach
10	chr1:212784200-212787400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:212784200-212788400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:212784200-212788600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr1:212784200-212788600	Weak transcription	Fetal Intestine Large	intestine
14	chr1:212784200-212789200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:212784200-212790400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:212784200-212796800	Weak transcription	Stomach Mucosa	stomach
17	chr1:212784400-212787800	Enhancers	Brain Hippocampus Middle	brain
18	chr1:212784400-212788000	Weak transcription	Fetal Stomach	stomach
19	chr1:212784400-212788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:212784400-212790200	Weak transcription	Dnd41	blood
21	chr1:212784400-212790400	Weak transcription	Colonic Mucosa	Colon
22	chr1:212784600-212788200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:212784600-212788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:212784600-212788400	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:212784600-212788400	Weak transcription	Colon Smooth Muscle	Colon
26	chr1:212784600-212788400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:212784600-212788400	Weak transcription	NHEK	skin
28	chr1:212784600-212788800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:212784800-212787400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:212784800-212787600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr1:212784800-212788400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:212784800-212790400	Weak transcription	Brain Angular Gyrus	brain
33	chr1:212784800-212794800	Weak transcription	NH-A	brain
34	chr1:212785000-212787200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:212785000-212787600	Enhancers	H1 Cell Line	embryonic stem cell
36	chr1:212785000-212787600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:212785000-212787600	Enhancers	Placenta	Placenta
38	chr1:212785000-212787600	Weak transcription	Right Ventricle	heart
39	chr1:212785000-212787600	Weak transcription	K562	blood
40	chr1:212785000-212787800	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr1:212785000-212787800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:212785000-212787800	Enhancers	NHDF-Ad	bronchial
43	chr1:212785000-212787800	Enhancers	Osteobl	bone
44	chr1:212785000-212788200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:212785000-212788200	Weak transcription	Liver	Liver
46	chr1:212785000-212788200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:212785000-212788400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:212785000-212788400	Weak transcription	Hela-S3	cervix
49	chr1:212785000-212788600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:212785000-212790200	Weak transcription	Psoas Muscle	Psoas

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