Variant report

Variant	rs2542776
Chromosome Location	chr9:86294533-86294534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86293365..86298412-chr9:86320425..86323449,5	MCF-7	breast:
2	chr9:86294482..86296558-chr9:86300317..86302539,2	MCF-7	breast:
3	chr9:86290754..86292559-chr9:86294512..86296135,2	MCF-7	breast:
4	chr9:86290356..86292978-chr9:86293291..86295310,2	K562	blood:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10115799	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10119344	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10125432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1035274	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1044175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746718	1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs10746719	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746721	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10780621	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11140198	0.85[CHB][hapmap]
rs11140209	0.84[CHB][hapmap];0.82[ASN][1000 genomes]
rs11791175	0.85[CHB][hapmap]
rs1333863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1360685	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1413293	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1537503	0.85[CHB][hapmap]
rs1572135	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1889260	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1961952	0.82[EUR][1000 genomes]
rs1968216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042042	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2542803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780969	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2780972	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2780975	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2780982	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2780995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780997	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780998	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2780999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781000	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2781001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2781003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811909	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2811912	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2811919	0.89[ASN][1000 genomes]
rs2811921	0.85[CHB][hapmap]
rs2811922	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811924	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2811925	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2811931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4146741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4454364	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4877263	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4877796	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs4877798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6559739	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7023082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039019	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7469301	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7850944	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7860614	0.82[ASN][1000 genomes]
rs7863266	0.81[ASN][1000 genomes]
rs7865296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs944946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs961807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:86263400-86298800	Strong transcription	Fetal Thymus	thymus
3	chr9:86264600-86297000	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr9:86264800-86294600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:86264800-86295600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:86264800-86298200	Strong transcription	Dnd41	blood
7	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:86265000-86295200	Strong transcription	HSMM	muscle
9	chr9:86265000-86296800	Strong transcription	Liver	Liver
10	chr9:86265000-86298800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:86266200-86296000	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr9:86266400-86298800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr9:86267400-86296800	Strong transcription	A549	lung
14	chr9:86267400-86297800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr9:86267600-86296800	Strong transcription	Primary hematopoietic stem cells	blood
16	chr9:86267800-86295400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr9:86268000-86295400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:86268000-86298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:86268200-86294800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr9:86269200-86297800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:86269400-86298600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:86270400-86295400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr9:86270800-86298000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:86271200-86298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:86273600-86298600	Weak transcription	Stomach Mucosa	stomach
26	chr9:86273600-86299000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:86273800-86304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:86276200-86295400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr9:86279800-86299200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:86281600-86298800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr9:86282000-86298800	Strong transcription	Primary B cells from peripheral blood	blood
33	chr9:86282000-86299000	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:86282000-86300000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr9:86282400-86297000	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr9:86282400-86298000	Strong transcription	Primary B cells from cord blood	blood
37	chr9:86282800-86296800	Strong transcription	Stomach Smooth Muscle	stomach
38	chr9:86282800-86297800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr9:86283000-86297800	Strong transcription	Adipose Nuclei	Adipose
40	chr9:86283000-86298000	Strong transcription	HUVEC	blood vessel
41	chr9:86283000-86298200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr9:86283200-86297400	Strong transcription	Primary T cells from cord blood	blood
43	chr9:86283400-86295600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:86283400-86298000	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr9:86283400-86298000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr9:86283400-86299000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr9:86284000-86294800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr9:86284000-86298000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr9:86284800-86294800	Strong transcription	GM12878-XiMat	blood
50	chr9:86284800-86298000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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