Variant report

Variant	rs9904797
Chromosome Location	chr17:60024858-60024859
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60005709..60008113-chr17:60023114..60025647,2	MCF-7	breast:
2	chr17:60001930..60007756-chr17:60014153..60029774,25	MCF-7	breast:
3	chr17:60022419..60025195-chr17:60026545..60029743,3	K562	blood:
4	chr17:60023206..60027330-chr17:60041588..60045632,3	MCF-7	breast:
5	chr17:60023878..60028943-chr17:60030067..60035239,5	MCF-7	breast:
6	chr17:60017329..60019880-chr17:60023720..60025773,3	K562	blood:
7	chr17:60023310..60025821-chr17:60028190..60029965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs16945766	0.84[ASW][hapmap]
rs16945796	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs17400363	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs28435233	0.85[AFR][1000 genomes]
rs28442160	0.83[AFR][1000 genomes]
rs7214601	0.85[AFR][1000 genomes]
rs7219120	0.96[AFR][1000 genomes]
rs7225456	0.86[AFR][1000 genomes]
rs8076333	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9747362	0.89[AFR][1000 genomes]
rs9889643	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9892441	0.85[YRI][hapmap]
rs9893675	1.00[ASW][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9900745	0.84[ASW][hapmap];0.96[MKK][hapmap]
rs9905198	1.00[ASW][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9905273	0.87[AFR][1000 genomes]
rs9907648	0.84[ASW][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.82[AFR][1000 genomes]
rs9909731	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs9910165	0.89[AFR][1000 genomes]
rs9910404	1.00[YRI][hapmap]
rs9912291	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9915402	0.84[ASW][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap]
rs9916776	1.00[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60014200-60030000	Weak transcription	Stomach Mucosa	stomach
2	chr17:60014800-60028000	Weak transcription	Colonic Mucosa	Colon
3	chr17:60016000-60029800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr17:60016400-60027800	Weak transcription	Right Ventricle	heart
5	chr17:60017000-60027800	Weak transcription	Gastric	stomach
6	chr17:60017400-60026600	Weak transcription	Spleen	Spleen
7	chr17:60017600-60033800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr17:60017800-60033600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:60017800-60050400	Strong transcription	Adipose Nuclei	Adipose
10	chr17:60018000-60046800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:60018000-60072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:60018000-60073400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr17:60018200-60034400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:60018400-60034000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:60018400-60034000	Strong transcription	Placenta	Placenta
16	chr17:60018600-60047000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr17:60018600-60047200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr17:60018600-60072600	Strong transcription	Fetal Thymus	thymus
19	chr17:60018800-60073600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr17:60019000-60040000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr17:60019200-60026600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:60019200-60051600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr17:60019400-60025600	Strong transcription	Hela-S3	cervix
24	chr17:60019400-60030400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr17:60019600-60033800	Strong transcription	NH-A	brain
26	chr17:60019600-60034200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr17:60019600-60050600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:60020200-60050400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr17:60020400-60026600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:60020400-60050600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr17:60020400-60073200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr17:60020600-60026600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr17:60020600-60026600	Weak transcription	Esophagus	oesophagus
34	chr17:60020600-60026600	Weak transcription	Psoas Muscle	Psoas
35	chr17:60020600-60027400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:60020600-60027800	Weak transcription	Pancreas	Pancrea
37	chr17:60020600-60030600	Weak transcription	Fetal Heart	heart
38	chr17:60020600-60034000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:60020600-60034000	Strong transcription	Primary B cells from cord blood	blood
40	chr17:60020600-60034000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr17:60020600-60043400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:60020600-60047200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr17:60020600-60073000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr17:60020800-60026000	Weak transcription	Aorta	Aorta
45	chr17:60020800-60033600	Strong transcription	Fetal Lung	lung
46	chr17:60020800-60034000	Strong transcription	HSMM	muscle
47	chr17:60020800-60051800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr17:60020800-60073800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr17:60021000-60033600	Strong transcription	Primary hematopoietic stem cells	blood
50	chr17:60021000-60033800	Strong transcription	HMEC	breast

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