Variant report

Variant	rs3748645
Chromosome Location	chr1:46035470-46035471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45825402..45826091-chr1:46035456..46036417,4	K562	blood:
2	chr1:46014904..46020261-chr1:46034308..46041374,10	K562	blood:
3	chr1:45977966..45978850-chr1:46035453..46036256,5	MCF-7	breast:
4	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:
5	chr1:46014904..46019071-chr1:46034504..46037164,4	K562	blood:
6	chr1:45987156..45987941-chr1:46035466..46036356,2	K562	blood:
7	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
8	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
9	chr1:46034190..46037574-chr1:46047982..46052662,9	K562	blood:
10	chr1:45804838..45807307-chr1:46034691..46038164,3	K562	blood:
11	chr1:46035115..46037673-chr1:46042096..46043959,2	K562	blood:
12	chr1:45185476..45188775-chr1:46033224..46037144,6	K562	blood:
13	chr1:45984510..45988941-chr1:46031540..46035902,8	MCF-7	breast:
14	chr1:46029652..46033129-chr1:46033927..46038189,5	K562	blood:
15	chr1:46035047..46037595-chr1:46039672..46041229,2	MCF-7	breast:
16	chr1:45977968..45978937-chr1:46035446..46036373,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117448	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000199377	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11590549	0.88[JPT][hapmap]
rs11808204	1.00[CEU][hapmap]
rs2275084	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs2297652	0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs28365868	1.00[EUR][1000 genomes]
rs28365913	1.00[EUR][1000 genomes]
rs3811433	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811434	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes]
rs41269109	1.00[EUR][1000 genomes]
rs41269111	1.00[EUR][1000 genomes]
rs41269115	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41272133	1.00[EUR][1000 genomes]
rs41312018	1.00[EUR][1000 genomes]
rs56215132	1.00[EUR][1000 genomes]
rs56220330	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
4	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
5	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
6	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
7	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46017800-46038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:46018000-46038600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:46018200-46037400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:46018400-46036400	Strong transcription	Fetal Stomach	stomach
5	chr1:46018400-46036800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:46018400-46036800	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:46018400-46036800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:46018400-46037000	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:46018600-46036800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr1:46018600-46037600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:46018600-46038200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr1:46022800-46036800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:46023000-46036600	Strong transcription	Dnd41	blood
14	chr1:46023400-46037200	Weak transcription	Psoas Muscle	Psoas
15	chr1:46024400-46037200	Strong transcription	Fetal Muscle Leg	muscle
16	chr1:46024600-46036800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:46025800-46035800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:46025800-46036600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:46025800-46036800	Strong transcription	Fetal Thymus	thymus
20	chr1:46025800-46036800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:46025800-46037800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:46026600-46035600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:46026800-46037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:46026800-46038600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:46028000-46036000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr1:46028200-46037400	Strong transcription	Fetal Intestine Large	intestine
27	chr1:46028200-46038800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:46029400-46037200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:46029600-46036800	Strong transcription	GM12878-XiMat	blood
30	chr1:46029800-46036800	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr1:46031000-46036800	Strong transcription	Osteobl	bone
32	chr1:46031200-46036400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:46031200-46036800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:46031200-46036800	Strong transcription	Fetal Brain Female	brain
35	chr1:46031400-46036600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:46031400-46036800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:46031400-46036800	Strong transcription	Primary T cells from cord blood	blood
38	chr1:46031400-46036800	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:46031400-46037000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:46031400-46037400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:46031400-46037400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:46031600-46035600	Strong transcription	K562	blood
43	chr1:46031600-46035800	Strong transcription	Colonic Mucosa	Colon
44	chr1:46031600-46036400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:46031600-46036600	Strong transcription	HepG2	liver
46	chr1:46031600-46037400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:46031800-46035800	Strong transcription	Aorta	Aorta
48	chr1:46032000-46035600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:46032000-46035800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:46032000-46035800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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