Variant report

Variant	rs12602103
Chromosome Location	chr17:59913158-59913159
allele	G/T
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:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59489492..59490333-chr17:59913089..59913811,3	MCF-7	breast:
2	chr17:59650869..59653370-chr17:59912861..59915398,2	MCF-7	breast:
3	chr17:59910683..59913384-chr17:59939792..59942548,3	K562	blood:
4	chr17:59655679..59662005-chr17:59908866..59914904,7	MCF-7	breast:
5	chr17:59893631..59896024-chr17:59912153..59913818,2	MCF-7	breast:
6	chr17:59731140..59732709-chr17:59911539..59913325,2	MCF-7	breast:
7	chr17:59485300..59495746-chr17:59906301..59920408,36	MCF-7	breast:
8	chr17:59913094..59914791-chr20:60639929..60642235,2	MCF-7	breast:
9	chr17:59910379..59913191-chr20:55840905..55842776,2	MCF-7	breast:
10	chr17:59524968..59526550-chr17:59911521..59913626,2	MCF-7	breast:
11	chr17:59898858..59900358-chr17:59911804..59913981,2	MCF-7	breast:
12	chr17:59711773..59715620-chr17:59912402..59915431,182	MCF-7	breast:
13	chr1:149222304..149225079-chr17:59912724..59914437,2	MCF-7	breast:
14	chr17:59486004..59494842-chr17:59908668..59916445,28	MCF-7	breast:
15	chr17:59660380..59661037-chr17:59913024..59913836,2	MCF-7	breast:
16	chr17:59708854..59715538-chr17:59908174..59913185,10	MCF-7	breast:
17	chr17:59911897..59913724-chr20:55683374..55686261,2	MCF-7	breast:
18	chr17:59497346..59499681-chr17:59911621..59914856,3	MCF-7	breast:
19	chr17:59711578..59716020-chr17:59910074..59916640,13	MCF-7	breast:
20	chr17:59652578..59654171-chr17:59913004..59915141,2	MCF-7	breast:
21	chr17:59738736..59741211-chr17:59912822..59914383,2	MCF-7	breast:
22	chr17:59476759..59479299-chr17:59911039..59913181,3	MCF-7	breast:
23	chr17:59911219..59913384-chr17:59939792..59942139,2	K562	blood:
24	chr17:59910616..59917582-chr17:59936691..59943102,15	MCF-7	breast:
25	chr17:59644416..59645995-chr17:59912870..59914609,2	MCF-7	breast:
26	chr17:59911641..59916436-chr20:55839275..55842881,5	MCF-7	breast:
27	chr17:59676046..59678013-chr17:59912761..59915314,2	MCF-7	breast:
28	chr17:59765135..59767717-chr17:59913157..59914673,2	MCF-7	breast:
29	chr17:59833992..59836586-chr17:59910616..59913241,3	MCF-7	breast:
30	chr17:59718611..59721023-chr17:59912495..59915335,3	MCF-7	breast:
31	chr17:59866718..59868702-chr17:59911534..59913402,2	MCF-7	breast:
32	chr17:59713310..59713900-chr17:59912629..59913254,2	MCF-7	breast:
33	chr17:59716212..59718286-chr17:59910672..59913286,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000187013	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000130699	Chromatin interaction
ENSG00000267131	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10515212	0.88[CEU][hapmap]
rs11652477	0.88[CEU][hapmap]
rs12452396	0.93[CEU][hapmap]
rs16945665	0.89[CHB][hapmap]
rs17542001	0.88[CEU][hapmap]
rs17614124	0.88[CEU][hapmap]
rs2014444	0.89[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs2066962	0.88[CEU][hapmap]
rs2278813	0.88[CEU][hapmap]
rs4988340	0.89[CEU][hapmap];0.85[CHB][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs6504074	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223607	0.88[CEU][hapmap]
rs8075585	0.88[CEU][hapmap]
rs8076727	0.88[CEU][hapmap]
rs8076746	0.88[CEU][hapmap]

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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
3	nsv575841	chr17:59812748-59914681	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
4	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
5	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
6	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12602103	PTRH2	cis	cerebellum	SCAN
rs12602103	BRIP1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59863600-59925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
3	chr17:59884200-59933200	Weak transcription	K562	blood
4	chr17:59894000-59922400	Weak transcription	Osteobl	bone
5	chr17:59894800-59922000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr17:59898800-59914400	Weak transcription	Primary B cells from cord blood	blood
7	chr17:59898800-59920800	Weak transcription	Thymus	Thymus
8	chr17:59898800-59939600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr17:59898800-59939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:59899200-59919000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr17:59899400-59920600	Weak transcription	Fetal Thymus	thymus
12	chr17:59899400-59924200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr17:59904200-59927000	Weak transcription	Fetal Kidney	kidney
14	chr17:59904800-59933200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr17:59905400-59923800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr17:59905400-59931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:59905600-59923800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:59905800-59919000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr17:59905800-59920600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:59905800-59923600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:59905800-59939000	Weak transcription	Primary T cells from cord blood	blood
22	chr17:59906000-59914000	Weak transcription	HepG2	liver
23	chr17:59906000-59919200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr17:59906200-59921400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr17:59906200-59940200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr17:59906400-59919000	Weak transcription	GM12878-XiMat	blood
27	chr17:59906400-59919200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr17:59907800-59920200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:59909600-59913600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr17:59910000-59921200	Weak transcription	Fetal Muscle Leg	muscle
31	chr17:59910200-59918800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr17:59910600-59914400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr17:59911000-59914600	Enhancers	Fetal Lung	lung
34	chr17:59911200-59921000	Weak transcription	Fetal Stomach	stomach
35	chr17:59911600-59913600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr17:59911600-59914000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr17:59911600-59937800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr17:59911800-59939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr17:59912000-59913800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr17:59912000-59919200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:59912000-59919400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr17:59912000-59925600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr17:59912000-59938400	Weak transcription	HUVEC	blood vessel
44	chr17:59912200-59914200	Weak transcription	NHLF	lung
45	chr17:59912200-59921600	Weak transcription	NH-A	brain
46	chr17:59912200-59939200	Weak transcription	HSMM	muscle
47	chr17:59912200-59939800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr17:59912400-59914200	Weak transcription	A549	lung
49	chr17:59912400-59918400	Weak transcription	Hela-S3	cervix
50	chr17:59912400-59918800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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