Variant report

Variant	rs662602
Chromosome Location	chr1:120266903-120266904
allele	C/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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:120259669..120263744-chr1:120265349..120268007,3	K562	blood:
2	chr1:120262686..120264367-chr1:120265384..120267918,2	MCF-7	breast:
3	chr1:120266399..120268566-chr1:120269981..120272303,2	MCF-7	breast:
4	chr1:120266689..120269358-chr20:39499733..39501631,2	MCF-7	breast:
5	chr1:120257304..120259977-chr1:120266897..120269007,2	K562	blood:
6	chr1:120265174..120267871-chr1:120268528..120272472,4	K562	blood:
7	chr1:120266054..120268534-chr1:120274257..120277960,3	MCF-7	breast:
8	chr1:120265675..120267293-chr1:120269685..120271741,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1163251	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2764886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs477992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs478093	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs483180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487081	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs487884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs496195	0.83[ASN][1000 genomes]
rs496198	0.83[ASN][1000 genomes]
rs511059	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs514491	0.83[ASN][1000 genomes]
rs517533	0.83[ASN][1000 genomes]
rs532303	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs539708	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs541503	1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs561931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs592762	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs594400	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs595283	0.91[ASN][1000 genomes]
rs597308	0.83[ASN][1000 genomes]
rs598685	0.83[ASN][1000 genomes]
rs606312	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs611365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs612430	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs616111	0.82[ASN][1000 genomes]
rs627707	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs629735	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs637868	0.86[JPT][hapmap]
rs639216	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs639761	0.85[ASN][1000 genomes]
rs640195	0.85[ASN][1000 genomes]
rs658442	0.87[ASN][1000 genomes]
rs660073	0.87[ASN][1000 genomes]
rs662243	1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs666930	0.86[JPT][hapmap]
rs677277	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs839600	0.83[ASN][1000 genomes]
rs839605	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs866321	0.85[ASN][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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120256200-120267400	Weak transcription	Lung	lung
2	chr1:120256200-120271800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr1:120256400-120271800	Weak transcription	Gastric	stomach
4	chr1:120256400-120276800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr1:120256400-120284400	Weak transcription	GM12878-XiMat	blood
6	chr1:120256600-120275600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:120257000-120271800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:120257000-120277400	Weak transcription	Fetal Heart	heart
9	chr1:120257000-120278400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:120257000-120278600	Weak transcription	HSMM	muscle
11	chr1:120257000-120282400	Weak transcription	A549	lung
12	chr1:120257200-120287000	Weak transcription	NH-A	brain
13	chr1:120257600-120268000	Weak transcription	Fetal Brain Male	brain
14	chr1:120258600-120267200	Weak transcription	Fetal Brain Female	brain
15	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:120258800-120269400	Weak transcription	Spleen	Spleen
17	chr1:120258800-120275000	Weak transcription	Right Atrium	heart
18	chr1:120259200-120277800	Weak transcription	Right Ventricle	heart
19	chr1:120260400-120287600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:120261000-120274200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:120261000-120287200	Strong transcription	Hela-S3	cervix
22	chr1:120261200-120269400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:120261400-120268800	Weak transcription	Small Intestine	intestine
24	chr1:120261400-120274800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:120261600-120273600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:120261600-120288200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:120261800-120267800	Genic enhancers	HepG2	liver
28	chr1:120261800-120281600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:120261800-120287000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:120261800-120287600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:120262000-120273200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:120262000-120274600	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:120262000-120284600	Strong transcription	Fetal Stomach	stomach
34	chr1:120262000-120287200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:120262000-120287400	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:120262000-120287400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr1:120262000-120287800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:120262000-120288200	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:120262200-120273800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:120262200-120274400	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:120262200-120284400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:120262400-120279200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:120262400-120283600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:120262400-120285000	Strong transcription	NHEK	skin
45	chr1:120262400-120287400	Strong transcription	Dnd41	blood
46	chr1:120262400-120288200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:120262600-120271800	Genic enhancers	Fetal Intestine Small	intestine
48	chr1:120262600-120282800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr1:120262600-120283800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:120262800-120270200	Strong transcription	Adipose Nuclei	Adipose

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