Variant report

Variant	rs6504080
Chromosome Location	chr17:60109041-60109042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60107282..60111118-chr17:60141035..60143494,4	MCF-7	breast:
2	chr17:60106228..60109334-chr17:60110578..60113962,3	MCF-7	breast:
3	chr17:60107140..60109283-chr17:60113223..60115385,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction
ENSG00000200842	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs16945766	0.86[ASW][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs28479677	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7212884	1.00[MEX][hapmap]
rs7213026	1.00[MEX][hapmap]
rs7222876	1.00[MEX][hapmap]
rs73991955	0.80[AMR][1000 genomes]
rs73991962	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs9892063	1.00[MEX][hapmap]
rs9907648	0.86[ASW][hapmap]
rs9909882	1.00[MEX][hapmap]
rs9915402	0.86[ASW][hapmap]

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	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	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6504080	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
2	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
3	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
5	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:60094600-60113200	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:60095000-60112600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:60095000-60113200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr17:60095800-60112600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:60095800-60113000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:60096000-60113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:60097000-60113000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:60097000-60113000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:60098600-60111400	Strong transcription	Fetal Lung	lung
15	chr17:60098600-60112400	Strong transcription	Fetal Muscle Leg	muscle
16	chr17:60098600-60114600	Strong transcription	Placenta	Placenta
17	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:60098800-60111000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr17:60098800-60111600	Strong transcription	Thymus	Thymus
20	chr17:60098800-60112600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr17:60098800-60112800	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr17:60098800-60112800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:60098800-60113000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr17:60098800-60113200	Strong transcription	Adipose Nuclei	Adipose
25	chr17:60098800-60135000	Strong transcription	Dnd41	blood
26	chr17:60099000-60109600	Strong transcription	HUVEC	blood vessel
27	chr17:60099000-60111400	Strong transcription	Primary B cells from cord blood	blood
28	chr17:60099000-60111400	Strong transcription	Primary T cells from cord blood	blood
29	chr17:60099000-60111600	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr17:60099000-60111600	Strong transcription	Fetal Kidney	kidney
31	chr17:60099000-60111600	Strong transcription	A549	lung
32	chr17:60099000-60112800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr17:60099000-60113000	Strong transcription	Primary B cells from peripheral blood	blood
34	chr17:60099000-60113000	Strong transcription	HepG2	liver
35	chr17:60099000-60113200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr17:60099000-60113200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr17:60099000-60113200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr17:60099000-60113200	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:60099200-60113400	Strong transcription	K562	blood
41	chr17:60099400-60111600	Strong transcription	Fetal Intestine Large	intestine
42	chr17:60099400-60114200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:60099400-60114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:60100000-60111200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr17:60100600-60114200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr17:60100800-60111200	Strong transcription	Fetal Brain Female	brain
49	chr17:60102000-60111400	Strong transcription	Colon Smooth Muscle	Colon
50	chr17:60102600-60110000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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