Variant report

Variant	rs2808677
Chromosome Location	chr9:100473411-100473412
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100472331..100474659-chr9:100661495..100663570,2	MCF-7	breast:
2	chr9:100472975..100473600-chr9:100651604..100652809,3	MCF-7	breast:
3	chr9:100470983..100474278-chr9:100563427..100567562,3	MCF-7	breast:
4	chr9:100472803..100473512-chr9:100716512..100717511,2	MCF-7	breast:
5	chr9:100472959..100473568-chr9:100663208..100663905,3	MCF-7	breast:
6	chr9:100472796..100473492-chr9:100654276..100655463,5	MCF-7	breast:
7	chr9:100472419..100473515-chr9:100652192..100652909,5	K562	blood:
8	chr9:100468636..100471244-chr9:100471475..100473548,2	MCF-7	breast:
9	chr9:100469221..100472408-chr9:100472563..100475555,3	K562	blood:
10	chr9:100472637..100473577-chr9:100662994..100663928,6	K562	blood:
11	chr9:100472598..100473541-chr9:100662995..100663732,5	MCF-7	breast:
12	chr9:100457305..100459777-chr9:100472786..100474534,2	MCF-7	breast:
13	chr9:100465773..100467417-chr9:100473375..100476124,2	MCF-7	breast:
14	chr9:100471666..100473790-chr9:100684234..100685883,3	MCF-7	breast:
15	chr9:100466290..100468242-chr9:100471348..100474178,4	K562	blood:
16	chr9:100473102..100474630-chr9:100476302..100477871,2	K562	blood:
17	chr9:100471241..100474154-chr9:100481493..100483041,2	K562	blood:
18	chr9:100472702..100473627-chr9:100657597..100658729,4	MCF-7	breast:
19	chr9:100473042..100473573-chr9:100565746..100566684,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000136936	Chromatin interaction
ENSG00000136932	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10983030	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10983447	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12378130	0.84[ASN][1000 genomes]
rs12379552	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800975	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2026132	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2036959	0.85[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668792	0.93[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668793	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668798	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773347	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2773351	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2805767	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2805775	0.86[EUR][1000 genomes]
rs2805777	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2805779	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2805824	0.93[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2805825	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805826	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805829	0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805832	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2805837	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2805839	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2805840	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2808668	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2808673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2808675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2808683	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2808685	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808686	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808687	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808689	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808691	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2808692	0.93[EUR][1000 genomes]
rs2808694	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2808701	0.91[EUR][1000 genomes]
rs2808703	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6478325	0.85[EUR][1000 genomes]
rs7465737	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs958346	0.96[CEU][hapmap]

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	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1043753	chr9:100458109-100599265	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100467200-100476400	Weak transcription	Fetal Intestine Large	intestine
2	chr9:100468000-100476600	Weak transcription	GM12878-XiMat	blood
3	chr9:100471200-100476400	Weak transcription	Fetal Intestine Small	intestine
4	chr9:100472600-100473600	Enhancers	Hela-S3	cervix
5	chr9:100472600-100474000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr9:100472600-100474200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:100472800-100473600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr9:100472800-100473600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
9	chr9:100472800-100473600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:100472800-100473600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:100472800-100473600	Enhancers	A549	lung
12	chr9:100472800-100473800	Enhancers	HSMMtube	muscle
13	chr9:100472800-100476400	Weak transcription	HepG2	liver
14	chr9:100473000-100473600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:100473000-100473800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr9:100473000-100473800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr9:100473000-100474000	Enhancers	Primary T cells from cord blood	blood
18	chr9:100473000-100474000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr9:100473200-100473600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:100473200-100473600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
21	chr9:100473200-100473600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
22	chr9:100473200-100473600	Enhancers	Primary B cells from peripheral blood	blood
23	chr9:100473200-100473600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:100473200-100473600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:100473200-100473600	Bivalent Enhancer	Adipose Nuclei	Adipose
26	chr9:100473200-100473600	Enhancers	Brain Hippocampus Middle	brain
27	chr9:100473200-100473600	Bivalent Enhancer	Fetal Kidney	kidney
28	chr9:100473200-100473600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
29	chr9:100473200-100473600	Bivalent Enhancer	Fetal Thymus	thymus
30	chr9:100473200-100473600	Enhancers	HMEC	breast
31	chr9:100473200-100473600	Enhancers	NHEK	skin
32	chr9:100473200-100473800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:100473200-100473800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:100473200-100473800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr9:100473200-100473800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:100473200-100473800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:100473200-100473800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:100473200-100473800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:100473200-100473800	Enhancers	Fetal Heart	heart
40	chr9:100473200-100473800	Bivalent Enhancer	Fetal Muscle Leg	muscle
41	chr9:100473200-100473800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
42	chr9:100473200-100473800	Enhancers	HSMM	muscle
43	chr9:100473200-100474000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr9:100473200-100474000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr9:100473200-100474000	Enhancers	Primary hematopoietic stem cells	blood
46	chr9:100473200-100474000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
47	chr9:100473200-100474000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr9:100473200-100474000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr9:100473200-100474400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr9:100473400-100473600	Enhancers	ES-WA7 Cell Line	embryonic stem cell

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