Variant report

Variant	rs9988489
Chromosome Location	chr1:149979846-149979847
allele	C/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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:149853005..149861438-chr1:149978765..149991065,34	MCF-7	breast:
2	chr1:149978737..149980567-chr1:150038364..150039964,2	MCF-7	breast:
3	chr1:149855536..149863300-chr1:149977462..149985642,29	K562	blood:
4	chr1:149977821..149984701-chr1:150037094..150041280,13	MCF-7	breast:
5	chr1:149959534..149961755-chr1:149979589..149981330,2	MCF-7	breast:
6	chr1:149854540..149863300-chr1:149979575..149985253,19	K562	blood:
7	chr1:149896924..149901430-chr1:149978916..149983998,7	MCF-7	breast:
8	chr1:149979248..149981282-chr1:150121900..150123528,2	K562	blood:
9	chr1:149979408..149982385-chr1:150047127..150049336,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184260	Chromatin interaction
ENSG00000136631	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000143368	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10494259	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10494261	0.92[ASW][hapmap];0.88[MKK][hapmap]
rs1061955	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11205308	0.92[ASW][hapmap];0.91[MKK][hapmap]
rs11205313	0.81[YRI][hapmap];1.00[AMR][1000 genomes]
rs11205314	1.00[AMR][1000 genomes]
rs12022928	0.91[YRI][hapmap]
rs12060171	1.00[AMR][1000 genomes]
rs12060830	1.00[ASW][hapmap];0.94[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap]
rs12064434	0.90[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12082035	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091025	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091858	0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091904	1.00[AMR][1000 genomes]
rs16833063	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16833149	0.91[YRI][hapmap]
rs16833175	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16833178	0.92[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes]
rs16838432	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4279885	0.91[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58342123	1.00[AMR][1000 genomes]
rs74126211	1.00[AMR][1000 genomes]
rs7517085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9804143	0.85[ASW][hapmap];0.86[MKK][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831537	chr1:149833357-150064655	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	431 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:149948200-149981000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:149948400-149981400	Weak transcription	Esophagus	oesophagus
3	chr1:149952200-149980800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:149965000-149981400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:149967800-149981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:149968200-149980800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:149968400-149980800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:149968600-149980000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:149969000-149980800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:149969800-149981400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:149970000-149980400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:149970000-149981000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:149970000-149981000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr1:149970000-149981000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:149970200-149980000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:149970200-149980600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:149970600-149980000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:149972200-149980000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:149972800-149981600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:149973800-149980400	Weak transcription	Aorta	Aorta
21	chr1:149976200-149981400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:149976400-149980800	Weak transcription	Lung	lung
23	chr1:149977000-149980800	Enhancers	Fetal Heart	heart
24	chr1:149977000-149981400	Weak transcription	Placenta	Placenta
25	chr1:149977800-149980600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr1:149977800-149981000	Weak transcription	Fetal Brain Female	brain
27	chr1:149977800-149983200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:149978000-149980000	Weak transcription	Brain Germinal Matrix	brain
29	chr1:149978000-149980800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:149978000-149980800	Weak transcription	Fetal Brain Male	brain
31	chr1:149978000-149981400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:149978200-149980600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:149978400-149980800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:149978600-149980200	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr1:149978600-149980200	Enhancers	Ovary	ovary
36	chr1:149978600-149980200	Enhancers	Psoas Muscle	Psoas
37	chr1:149978600-149980200	Genic enhancers	NHEK	skin
38	chr1:149978600-149980400	Enhancers	HepG2	liver
39	chr1:149978600-149980600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:149978600-149980600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:149978600-149980600	Enhancers	Stomach Mucosa	stomach
42	chr1:149978600-149980800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:149978600-149980800	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr1:149978600-149980800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:149978600-149980800	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr1:149978600-149981200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:149978800-149980000	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:149978800-149980400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr1:149978800-149980400	Enhancers	Liver	Liver
50	chr1:149978800-149980600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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