Variant report

Variant	rs6504078
Chromosome Location	chr17:60048582-60048583
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60044150..60045918-chr17:60046685..60050147,3	MCF-7	breast:
2	chr17:60004304..60005911-chr17:60047973..60050646,2	MCF-7	breast:
3	chr17:60048420..60050765-chr17:60062376..60064938,2	MCF-7	breast:
4	chr17:60040110..60042878-chr17:60047051..60049770,2	MCF-7	breast:
5	chr17:60042806..60044901-chr17:60046957..60049761,2	K562	blood:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10221202	0.87[AFR][1000 genomes]
rs10401014	1.00[EUR][1000 genomes]
rs16945750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28431006	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4988342	1.00[EUR][1000 genomes]
rs58025472	1.00[EUR][1000 genomes]
rs58046635	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504075	1.00[EUR][1000 genomes]
rs6504076	1.00[EUR][1000 genomes]
rs7211128	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7212884	1.00[EUR][1000 genomes]
rs7213026	1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7221827	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7222876	1.00[EUR][1000 genomes]
rs7224112	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7226248	1.00[EUR][1000 genomes]
rs73991952	1.00[EUR][1000 genomes]
rs8065060	1.00[EUR][1000 genomes]
rs8068267	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069386	1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	1.00[EUR][1000 genomes]
rs9783837	0.90[AFR][1000 genomes]
rs9783841	1.00[EUR][1000 genomes]
rs9892063	1.00[EUR][1000 genomes]
rs9892123	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9892513	0.89[AMR][1000 genomes]
rs9894718	1.00[EUR][1000 genomes]
rs9896768	1.00[EUR][1000 genomes]
rs9899042	1.00[EUR][1000 genomes]
rs9899780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9902699	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903562	1.00[EUR][1000 genomes]
rs9905888	1.00[EUR][1000 genomes]
rs9909145	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909882	1.00[EUR][1000 genomes]
rs9910067	1.00[EUR][1000 genomes]
rs9910252	1.00[EUR][1000 genomes]
rs9910902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9914007	1.00[EUR][1000 genomes]
rs9914605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9944467	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60017800-60050400	Strong transcription	Adipose Nuclei	Adipose
2	chr17:60018000-60072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr17:60018000-60073400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:60018600-60072600	Strong transcription	Fetal Thymus	thymus
5	chr17:60018800-60073600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:60019200-60051600	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr17:60019600-60050600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:60020200-60050400	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr17:60020400-60050600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr17:60020400-60073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr17:60020600-60073000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:60020800-60051800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr17:60020800-60073800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:60021000-60050200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr17:60021200-60097000	Strong transcription	Dnd41	blood
16	chr17:60021800-60052400	Strong transcription	HepG2	liver
17	chr17:60021800-60073600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr17:60022000-60051800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr17:60022200-60052200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr17:60022200-60053200	Strong transcription	Fetal Intestine Large	intestine
21	chr17:60023200-60049400	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr17:60023600-60050600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr17:60025400-60074200	Strong transcription	Liver	Liver
24	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:60028400-60059600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr17:60032800-60058600	Weak transcription	Fetal Heart	heart
27	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
28	chr17:60033200-60056600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr17:60034800-60052200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr17:60034800-60072800	Strong transcription	Placenta	Placenta
31	chr17:60035400-60049000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr17:60035600-60049800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr17:60035600-60050000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:60035600-60050200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr17:60035600-60050200	Strong transcription	Primary B cells from peripheral blood	blood
36	chr17:60035800-60050200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr17:60035800-60064400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr17:60036000-60050200	Strong transcription	GM12878-XiMat	blood
39	chr17:60036000-60050400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:60036000-60074000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:60036200-60050600	Strong transcription	Osteobl	bone
42	chr17:60036400-60070000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr17:60036600-60050000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr17:60036800-60049400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr17:60038400-60059400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr17:60040400-60058800	Weak transcription	NHEK	skin
47	chr17:60041200-60048600	Strong transcription	Primary hematopoietic stem cells	blood
48	chr17:60042600-60058400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr17:60042600-60063600	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr17:60042800-60049000	Weak transcription	Small Intestine	intestine

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