Variant report

Variant	rs1534058
Chromosome Location	chr1:151009689-151009690
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151009679-151010075	HepG2	liver:	n/a	n/a
2	GATA3	chr1:151009582-151009917	T-47D	breast:	n/a	n/a
3	POLR2A	chr1:151009624-151010187	Hela-S3	cervix:	n/a	n/a
4	FOXA1	chr1:151009495-151009910	T-47D	breast:	n/a	n/a
5	POLR2A	chr1:151009528-151009765	MCF-7	breast:	n/a	n/a
6	POLR2A	chr1:151009632-151009882	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:151009652-151009750	K562	blood:	n/a	n/a
8	POLR2A	chr1:151008841-151010214	K562	blood:	n/a	n/a
9	SIN3AK20	chr1:151008713-151009997	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:151008538..151012828-chr1:151019200..151022428,4	K562	blood:
2	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
3	chr1:151008451..151011049-chr1:151011107..151015383,5	K562	blood:
4	chr1:150997115..151004935-chr1:151005196..151010372,8	MCF-7	breast:
5	chr1:150979416..150982558-chr1:151006468..151010604,5	MCF-7	breast:
6	chr1:151008899..151010447-chr1:151116259..151119248,2	MCF-7	breast:

No data

Variant related genes	Relation type
BNIPL	TF binding region
ENSG00000213190	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143443	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11799858	0.85[AMR][1000 genomes]
rs11799964	0.81[AFR][1000 genomes]
rs11799977	0.85[AMR][1000 genomes]
rs11803792	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11804787	0.85[AMR][1000 genomes]
rs11811879	0.85[AMR][1000 genomes]
rs1534059	0.86[AFR][1000 genomes];1.00[AMR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150989800-151010400	Strong transcription	Fetal Stomach	stomach
2	chr1:150996600-151009800	Strong transcription	Fetal Intestine Small	intestine
3	chr1:150997400-151009800	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:150997600-151015400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:150997600-151019800	Weak transcription	HUVEC	blood vessel
6	chr1:150997800-151019800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:150999200-151010000	Strong transcription	Fetal Brain Female	brain
8	chr1:151000000-151019800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:151000000-151019800	Weak transcription	NHLF	lung
10	chr1:151000200-151019800	Weak transcription	Small Intestine	intestine
11	chr1:151003000-151011400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:151003800-151019800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:151004400-151011400	Weak transcription	NHDF-Ad	bronchial
14	chr1:151004400-151015400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:151004400-151019800	Weak transcription	Fetal Kidney	kidney
16	chr1:151006800-151015400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:151006800-151019800	Weak transcription	Gastric	stomach
18	chr1:151006800-151019800	Weak transcription	HepG2	liver
19	chr1:151007000-151019000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr1:151007000-151019600	Weak transcription	Colonic Mucosa	Colon
21	chr1:151007200-151010600	Weak transcription	GM12878-XiMat	blood
22	chr1:151007200-151019800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:151007200-151019800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:151007400-151009800	Weak transcription	Hela-S3	cervix
25	chr1:151007400-151010600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:151007400-151015400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:151007400-151019600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:151007400-151019800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:151007400-151019800	Weak transcription	Brain Angular Gyrus	brain
30	chr1:151007400-151019800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:151007600-151015400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr1:151007600-151019600	Weak transcription	Fetal Brain Male	brain
33	chr1:151007800-151015400	Weak transcription	Spleen	Spleen
34	chr1:151007800-151015600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:151007800-151019000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:151007800-151019000	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:151007800-151019200	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:151008000-151015400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr1:151008000-151015400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:151008000-151015400	Weak transcription	HSMMtube	muscle
41	chr1:151008000-151015600	Weak transcription	Brain Substantia Nigra	brain
42	chr1:151008000-151018000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:151008000-151018000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr1:151008000-151019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:151008000-151019200	Weak transcription	Primary B cells from cord blood	blood
46	chr1:151008000-151019200	Weak transcription	Dnd41	blood
47	chr1:151008000-151019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:151008000-151019600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:151008000-151019600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr1:151008000-151019600	Weak transcription	Rectal Mucosa Donor 29	rectum

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