Variant report

Variant	rs1053316
Chromosome Location	chr1:222839838-222839839
allele	A/G
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:5)
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	POLR2A	chr1:222838576-222839967	HepG2	liver:	n/a	n/a
2	POLR2A	chr1:222829766-222841488	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:222832045..222836526-chr1:222836686..222840322,4	K562	blood:
2	chr1:222837697..222840012-chr1:222884469..222886731,2	K562	blood:
3	chr1:222815840..222818168-chr1:222838809..222840697,2	MCF-7	breast:
4	chr1:222837235..222840536-chr1:222884708..222887368,3	MCF-7	breast:
5	chr1:222812494..222814477-chr1:222837950..222840377,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272750	TF binding region
ENSG00000162819	Chromatin interaction
ENSG00000272750	Chromatin interaction
ENSG00000186063	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs17163384	0.82[MEX][hapmap]
rs17163431	0.82[MEX][hapmap]
rs2291833	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2936019	0.86[ASN][1000 genomes]
rs2936024	0.86[ASN][1000 genomes]
rs2936025	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs2936026	0.88[ASN][1000 genomes]
rs3002150	0.86[ASN][1000 genomes]
rs3008611	0.89[CHD][hapmap];0.85[JPT][hapmap]
rs3008613	0.85[JPT][hapmap]
rs3008620	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008624	0.84[ASN][1000 genomes]
rs3008627	0.86[ASN][1000 genomes]
rs3008628	0.86[ASN][1000 genomes]
rs3008632	0.86[ASN][1000 genomes]
rs3008633	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3008634	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008635	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs3008639	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs34290674	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs35684750	0.94[ASW][hapmap];0.95[CHD][hapmap];0.80[LWK][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs35762933	0.94[ASW][hapmap];0.95[CHD][hapmap];0.81[LWK][hapmap];0.99[MKK][hapmap];0.96[YRI][hapmap]
rs73124815	0.80[ASN][1000 genomes]
rs73124822	0.80[ASN][1000 genomes]
rs73124862	0.84[ASN][1000 genomes]
rs73124884	0.87[AFR][1000 genomes]
rs7520650	0.88[AFR][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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 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	chr1:222818800-222841600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:222819000-222841800	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:222819200-222841400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:222819200-222841600	Strong transcription	Placenta	Placenta
5	chr1:222819400-222841200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:222820000-222841400	Strong transcription	HSMM	muscle
7	chr1:222820000-222841600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:222820200-222841400	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:222820200-222841400	Strong transcription	NH-A	brain
10	chr1:222820400-222841800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:222820600-222841200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:222820600-222841400	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr1:222820800-222841000	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:222820800-222841200	Strong transcription	Fetal Intestine Large	intestine
15	chr1:222821000-222840000	Strong transcription	Fetal Kidney	kidney
16	chr1:222821200-222841400	Strong transcription	Adipose Nuclei	Adipose
17	chr1:222821400-222840000	Strong transcription	Fetal Brain Female	brain
18	chr1:222822200-222841200	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:222822200-222841400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:222822400-222841200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:222822400-222841400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:222822600-222840000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr1:222822600-222841400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:222822600-222841400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:222822800-222840800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr1:222823000-222841200	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:222823000-222841400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:222823200-222840000	Strong transcription	Brain Substantia Nigra	brain
29	chr1:222823200-222840600	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:222823200-222841400	Strong transcription	HepG2	liver
31	chr1:222823200-222841400	Strong transcription	K562	blood
32	chr1:222823400-222841400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:222824000-222841400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:222824000-222841400	Strong transcription	A549	lung
35	chr1:222825000-222841400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:222825600-222840000	Strong transcription	Left Ventricle	heart
37	chr1:222826800-222841400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:222827000-222845400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:222828400-222841400	Strong transcription	Hela-S3	cervix
40	chr1:222828400-222841600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:222828400-222841600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:222828600-222841200	Strong transcription	Fetal Thymus	thymus
43	chr1:222828800-222840800	Strong transcription	Osteobl	bone
44	chr1:222829000-222841000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:222829000-222841400	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:222829200-222840000	Strong transcription	Primary T cells from cord blood	blood
47	chr1:222829200-222841000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:222829200-222841400	Strong transcription	Primary B cells from cord blood	blood
49	chr1:222829200-222841400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr1:222829200-222841400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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