Variant report

Variant	rs9880744
Chromosome Location	chr3:105538599-105538600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:105536120..105538926-chr3:105539288..105541038,2	MCF-7	breast:
2	chr3:105538204..105540971-chr3:105547311..105549205,2	K562	blood:
3	chr3:105531033..105533636-chr3:105537856..105539546,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11919893	0.84[CEU][hapmap]
rs12485832	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487841	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496588	1.00[CEU][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12497428	0.83[CEU][hapmap]
rs12632980	0.83[CEU][hapmap]
rs13090949	0.84[CEU][hapmap]
rs13433776	0.84[CEU][hapmap]
rs2455887	0.86[ASN][1000 genomes]
rs3772512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56344829	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58882222	0.86[ASN][1000 genomes]
rs6437616	0.89[CEU][hapmap]
rs6437623	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766168	0.81[CEU][hapmap]
rs6778745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780432	0.83[CEU][hapmap]
rs6791765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793018	1.00[ASN][1000 genomes]
rs6796362	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997629	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997684	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7634195	0.84[CEU][hapmap]
rs7638504	0.83[CEU][hapmap]
rs7639888	1.00[CEU][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7641825	0.94[YRI][hapmap]
rs7649466	0.95[YRI][hapmap]
rs7650147	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894541	0.84[CEU][hapmap]
rs9657910	1.00[CHB][hapmap]
rs9811776	0.84[CEU][hapmap]
rs9814582	0.83[CEU][hapmap]
rs9820060	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838755	0.83[CEU][hapmap]
rs9841798	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872895	0.83[CEU][hapmap]
rs9876110	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[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	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
4	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:105519200-105541600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:105521200-105546800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:105521400-105541200	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:105521400-105542000	Weak transcription	Fetal Stomach	stomach
9	chr3:105522400-105541200	Weak transcription	Primary T cells from cord blood	blood
10	chr3:105524600-105541600	Weak transcription	Right Atrium	heart
11	chr3:105525600-105540200	Weak transcription	NHLF	lung
12	chr3:105526200-105541600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:105526200-105542400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:105528400-105541600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:105528400-105542000	Weak transcription	Pancreas	Pancrea
16	chr3:105528400-105543200	Weak transcription	Gastric	stomach
17	chr3:105528400-105553600	Weak transcription	Fetal Kidney	kidney
18	chr3:105528600-105542600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:105528800-105539000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:105528800-105539000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:105528800-105540000	Weak transcription	Fetal Heart	heart
22	chr3:105528800-105540200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:105528800-105541600	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:105529000-105540000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:105529000-105541600	Weak transcription	Fetal Lung	lung
26	chr3:105529000-105541800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:105529000-105542200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:105529000-105546600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:105530400-105540400	Weak transcription	Adipose Nuclei	Adipose
30	chr3:105530400-105541600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:105530400-105542000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:105530600-105540400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr3:105530600-105541800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr3:105530800-105541800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:105531400-105539200	Weak transcription	Liver	Liver
36	chr3:105531400-105540200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:105531400-105540200	Weak transcription	HSMMtube	muscle
38	chr3:105531400-105546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr3:105531600-105539000	Weak transcription	HSMM	muscle
40	chr3:105531600-105540400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:105531600-105541800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:105531600-105541800	Weak transcription	HMEC	breast
43	chr3:105531600-105546400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:105532000-105540000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:105532200-105540600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:105532200-105541800	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:105532200-105563000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:105532800-105540200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:105532800-105541200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:105532800-105542000	Weak transcription	HUVEC	blood vessel

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