Variant report

Variant	rs3768549
Chromosome Location	chr1:213033008-213033009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:213032868-213034975	K562	blood:	n/a	chr1:213033557-213033570 chr1:213033559-213033566
2	POLR2A	chr1:213033007-213034945	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:213032255..213037228-chr1:213037322..213040248,4	K562	blood:
2	chr1:213027721..213030641-chr1:213032667..213035705,3	K562	blood:
3	chr1:213029061..213031968-chr1:213032486..213034078,2	K562	blood:
4	chr1:213025871..213028763-chr1:213030169..213033277,3	MCF-7	breast:
5	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:
6	chr1:212965461..212968054-chr1:213031452..213034127,2	MCF-7	breast:
7	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
8	chr1:212977806..212980707-chr1:213030715..213033244,2	K562	blood:
9	chr1:213031674..213033675-chr1:213035938..213038632,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000236317	TF binding region
FLVCR1-AS1	TF binding region
FLVCR1	TF binding region
ENSG00000162772	Chromatin interaction
ENSG00000235182	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000236317	Chromatin interaction
ENSG00000162769	Chromatin interaction
ENSG00000198468	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2047288	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047291	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088256	1.00[AFR][1000 genomes]
rs3738799	1.00[AMR][1000 genomes]
rs3738801	1.00[AMR][1000 genomes]
rs41258005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275386	1.00[AMR][1000 genomes]
rs41296666	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296668	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296674	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296676	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41297452	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300027	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300033	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300035	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300043	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300979	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301029	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41307644	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41307646	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41314540	1.00[AMR][1000 genomes]
rs41314542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56300028	0.85[AMR][1000 genomes]
rs58746017	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73079880	0.85[AMR][1000 genomes]
rs73079886	0.85[AMR][1000 genomes]
rs73079887	0.85[AMR][1000 genomes]
rs7521050	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	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213029600-213033200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:213029600-213033400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:213030400-213033400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:213030400-213034000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:213030400-213034000	Active TSS	HSMM	muscle
6	chr1:213030400-213034600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:213030400-213035600	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:213030600-213033200	Active TSS	A549	lung
9	chr1:213030600-213033800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:213030600-213034000	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:213030600-213034000	Active TSS	GM12878-XiMat	blood
12	chr1:213030600-213034400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:213030600-213035000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:213030800-213033400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:213030800-213033400	Active TSS	HSMMtube	muscle
16	chr1:213030800-213033800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr1:213030800-213033800	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr1:213030800-213034200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:213030800-213035200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:213031000-213033400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:213031200-213033200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:213031200-213033400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:213031800-213033600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:213032000-213033200	Active TSS	Brain Germinal Matrix	brain
25	chr1:213032000-213033400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
26	chr1:213032000-213033600	Flanking Active TSS	HMEC	breast
27	chr1:213032000-213034000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:213032000-213034000	Flanking Active TSS	Dnd41	blood
29	chr1:213032200-213033200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr1:213032200-213033400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:213032200-213033400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:213032200-213033600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:213032200-213033600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr1:213032200-213033600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:213032200-213033600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:213032200-213033600	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr1:213032200-213034000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr1:213032200-213034200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr1:213032400-213034600	Enhancers	Spleen	Spleen
40	chr1:213032600-213033200	Active TSS	Brain Anterior Caudate	brain
41	chr1:213032600-213033200	Weak transcription	Small Intestine	intestine
42	chr1:213032600-213033200	Active TSS	HepG2	liver
43	chr1:213032600-213033200	Active TSS	NHEK	skin
44	chr1:213032600-213033200	Active TSS	Osteobl	bone
45	chr1:213032600-213033400	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr1:213032600-213033400	Weak transcription	Stomach Mucosa	stomach
47	chr1:213032600-213033400	Active TSS	Stomach Smooth Muscle	stomach
48	chr1:213032600-213033600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:213032600-213033600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:213032600-213033600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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