Variant report

Variant	rs3754048
Chromosome Location	chr1:150242189-150242190
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:150240625-150242429	HUVEC	blood vessel:	n/a	n/a
2	HCFC1	chr1:150240177-150242269	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:150239980-150242202	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr1:150240462-150242354	H1-neurons	neurons:	n/a	n/a
5	POLR2A	chr1:150242173-150242203	HepG2	liver:	n/a	n/a
6	GABPA	chr1:150240306-150242241	MCF-7	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150207289..150210046-chr1:150241185..150243177,3	MCF-7	breast:
2	chr1:150240799..150242755-chr1:150334348..150335863,2	MCF-7	breast:
3	chr1:150204090..150209498-chr1:150239337..150243073,9	K562	blood:
4	chr1:150240546..150242221-chr1:150264940..150266566,2	K562	blood:
5	chr1:150206345..150209742-chr1:150239312..150243074,6	K562	blood:
6	chr1:150240117..150242604-chr1:150335915..150338709,4	MCF-7	breast:
7	chr1:150240223..150242953-chr1:150263372..150266971,3	K562	blood:
8	chr1:150121990..150123693-chr1:150240466..150243151,2	K562	blood:
9	chr1:149855851..149859969-chr1:150239672..150242215,4	MCF-7	breast:
10	chr1:150206579..150210456-chr1:150238390..150242863,9	MCF-7	breast:

No data

Variant related genes	Relation type
APH1A	TF binding region
C1orf54	TF binding region
ENSG00000143401	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000222222	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000187145	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10888577	0.94[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11205347	0.82[CEU][hapmap]
rs11205350	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11205353	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12057558	0.87[ASN][1000 genomes]
rs12122277	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12133238	0.81[CEU][hapmap]
rs13374013	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13374483	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3118124	0.82[CEU][hapmap]
rs34908293	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35938158	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3850839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6668679	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7535712	0.82[CEU][hapmap]
rs7555995	0.88[CEU][hapmap]

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	nsv529719	chr1:150006344-150311095	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
3	nsv872415	chr1:150210538-150248046	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1009508	chr1:150211112-150270830	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv535154	chr1:150214907-150265508	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv1011223	chr1:150229205-150279380	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150239800-150242600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:150240000-150242400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:150240000-150242400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr1:150240000-150242400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr1:150240000-150242600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:150240200-150242200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:150240200-150242200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:150240200-150242200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:150240200-150242400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:150240400-150242200	Active TSS	A549	lung
11	chr1:150240400-150242200	Active TSS	HSMM	muscle
12	chr1:150240600-150242200	Active TSS	H1 Cell Line	embryonic stem cell
13	chr1:150240600-150242200	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:150240600-150242200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:150240600-150242200	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:150240600-150242200	Active TSS	Brain Angular Gyrus	brain
17	chr1:150240600-150242200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:150240600-150242200	Active TSS	Right Atrium	heart
19	chr1:150240600-150242200	Active TSS	Thymus	Thymus
20	chr1:150240600-150242200	Active TSS	HMEC	breast
21	chr1:150240600-150242200	Active TSS	NHEK	skin
22	chr1:150240600-150242400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:150240800-150242200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:150240800-150242200	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:150240800-150242200	Active TSS	Colon Smooth Muscle	Colon
26	chr1:150240800-150242400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:150240800-150242400	Active TSS	Brain Anterior Caudate	brain
28	chr1:150240800-150242400	Active TSS	Brain Hippocampus Middle	brain
29	chr1:150240800-150242400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr1:150240800-150242600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:150241000-150242200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:150241000-150242200	Active TSS	Brain Substantia Nigra	brain
33	chr1:150241200-150242200	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:150241200-150242400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:150241400-150242200	Active TSS	Brain Germinal Matrix	brain
36	chr1:150241400-150242400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:150241600-150242200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
38	chr1:150241600-150242200	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr1:150241600-150242200	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr1:150241600-150242200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr1:150241600-150242200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:150241600-150242200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:150241600-150242200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:150241600-150242200	Flanking Active TSS	Fetal Thymus	thymus
45	chr1:150241600-150242200	Flanking Active TSS	Dnd41	blood
46	chr1:150241600-150242200	Flanking Active TSS	Hela-S3	cervix
47	chr1:150241600-150242200	Flanking Active TSS	Osteobl	bone
48	chr1:150241600-150242400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:150241600-150242600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:150241600-150242600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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