Variant report

Variant	rs9899780
Chromosome Location	chr17:60106854-60106855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:60106228..60109334-chr17:60110578..60113962,3	MCF-7	breast:
2	chr17:60105875..60108705-chr17:60141999..60144284,3	MCF-7	breast:
3	chr17:60104559..60106878-chr17:60112435..60115169,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-INTS2-4	chr17:60106638-60108850	NONHSAT055142

Variant related genes	Relation type
ENSG00000200842	Chromatin interaction
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10401014	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16945750	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2278812	0.80[ASW][hapmap]
rs28431006	0.93[ASW][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4988342	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs58025472	1.00[EUR][1000 genomes]
rs58046635	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59794823	1.00[EUR][1000 genomes]
rs6504075	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6504076	1.00[EUR][1000 genomes]
rs6504078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7211128	1.00[EUR][1000 genomes]
rs7212399	1.00[EUR][1000 genomes]
rs7212824	0.93[ASW][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7212884	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7213026	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7217530	1.00[EUR][1000 genomes]
rs7217907	1.00[EUR][1000 genomes]
rs7221827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7222876	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7224112	1.00[EUR][1000 genomes]
rs7226248	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73991952	1.00[EUR][1000 genomes]
rs8065060	1.00[EUR][1000 genomes]
rs8068267	0.87[ASW][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8069386	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs8069903	1.00[EUR][1000 genomes]
rs8069946	1.00[EUR][1000 genomes]
rs8078342	1.00[EUR][1000 genomes]
rs9783841	1.00[EUR][1000 genomes]
rs9892063	1.00[TSI][hapmap];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[TSI][hapmap];1.00[EUR][1000 genomes]
rs9902699	0.84[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	0.93[ASW][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9909882	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9910067	1.00[EUR][1000 genomes]
rs9910252	1.00[EUR][1000 genomes]
rs9910451	0.87[ASW][hapmap]
rs9910902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9913351	0.93[ASW][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap]
rs9914007	1.00[EUR][1000 genomes]
rs9914605	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9915023	1.00[EUR][1000 genomes]
rs9916070	0.80[LWK][hapmap];1.00[TSI][hapmap]
rs9944467	1.00[EUR][1000 genomes]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60025400-60107600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
3	chr17:60069200-60107600	Weak transcription	Spleen	Spleen
4	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
5	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
7	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr17:60088400-60107600	Weak transcription	Pancreas	Pancrea
9	chr17:60094600-60113200	Strong transcription	Duodenum Smooth Muscle	Duodenum
10	chr17:60095000-60112600	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr17:60095000-60113200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr17:60095800-60112600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:60095800-60113000	Strong transcription	Fetal Muscle Trunk	muscle
14	chr17:60096000-60113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:60097000-60113000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr17:60097000-60113000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr17:60098600-60111400	Strong transcription	Fetal Lung	lung
18	chr17:60098600-60112400	Strong transcription	Fetal Muscle Leg	muscle
19	chr17:60098600-60114600	Strong transcription	Placenta	Placenta
20	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr17:60098800-60107600	Strong transcription	Liver	Liver
22	chr17:60098800-60111000	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr17:60098800-60111600	Strong transcription	Thymus	Thymus
24	chr17:60098800-60112600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr17:60098800-60112800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr17:60098800-60112800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:60098800-60113000	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr17:60098800-60113200	Strong transcription	Adipose Nuclei	Adipose
29	chr17:60098800-60135000	Strong transcription	Dnd41	blood
30	chr17:60099000-60107600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr17:60099000-60109600	Strong transcription	HUVEC	blood vessel
32	chr17:60099000-60111400	Strong transcription	Primary B cells from cord blood	blood
33	chr17:60099000-60111400	Strong transcription	Primary T cells from cord blood	blood
34	chr17:60099000-60111600	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr17:60099000-60111600	Strong transcription	Fetal Kidney	kidney
36	chr17:60099000-60111600	Strong transcription	A549	lung
37	chr17:60099000-60112800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:60099000-60113000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr17:60099000-60113000	Strong transcription	HepG2	liver
40	chr17:60099000-60113200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr17:60099000-60113200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr17:60099000-60113200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr17:60099000-60113200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:60099200-60113400	Strong transcription	K562	blood
46	chr17:60099400-60111600	Strong transcription	Fetal Intestine Large	intestine
47	chr17:60099400-60114200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr17:60099400-60114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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