Variant report

Variant	rs2777349
Chromosome Location	chr9:104169237-104169238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:104165233..104170505-chr9:104171045..104175682,8	MCF-7	breast:
2	chr9:104167280..104171241-chr9:104178855..104183117,5	K562	blood:
3	chr9:104160803..104165206-chr9:104167116..104171399,6	K562	blood:
4	chr9:104167820..104171241-chr9:104178855..104183117,4	K562	blood:

Variant related genes	Relation type
ENSG00000136897	Chromatin interaction
ENSG00000136870	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1233983	0.97[ASN][1000 genomes]
rs2777342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2777348	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4535787	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4577	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs475348	0.96[ASN][1000 genomes]
rs476046	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480792	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs491979	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs504023	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs506571	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs525998	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs535453	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546577	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs554157	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs571617	0.83[JPT][hapmap]
rs577823	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs578597	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap];0.97[ASN][1000 genomes]
rs578770	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs681	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852444	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2777349	ANKS6	cis	cerebellum	SCAN
rs2777349	XPA	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104162000-104169600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:104162600-104170400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:104162600-104170400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:104162600-104171600	Strong transcription	Placenta	Placenta
5	chr9:104162600-104172000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:104162800-104169400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr9:104162800-104169600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:104162800-104170000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr9:104162800-104170000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr9:104162800-104172200	ZNF genes & repeats	A549	lung
11	chr9:104162800-104173800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:104163000-104169600	Strong transcription	Fetal Thymus	thymus
13	chr9:104163000-104169800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:104163000-104173000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr9:104163200-104170200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:104163200-104172600	ZNF genes & repeats	Primary B cells from cord blood	blood
17	chr9:104163200-104174000	ZNF genes & repeats	Fetal Lung	lung
18	chr9:104163400-104172200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
19	chr9:104163400-104174000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:104163600-104170600	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr9:104163600-104173600	ZNF genes & repeats	Ovary	ovary
22	chr9:104164000-104170000	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr9:104164000-104173600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:104164200-104172200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:104164400-104171800	ZNF genes & repeats	Dnd41	blood
26	chr9:104164400-104172000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:104164400-104173400	ZNF genes & repeats	Colon Smooth Muscle	Colon
28	chr9:104164600-104173600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:104164600-104173800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr9:104164800-104173400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
31	chr9:104164800-104174200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:104164800-104174200	ZNF genes & repeats	Brain Hippocampus Middle	brain
33	chr9:104164800-104175400	ZNF genes & repeats	Fetal Muscle Leg	muscle
34	chr9:104165000-104173800	ZNF genes & repeats	Liver	Liver
35	chr9:104165200-104170200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:104165200-104172000	ZNF genes & repeats	Fetal Intestine Large	intestine
37	chr9:104165200-104172000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
38	chr9:104165200-104172200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
39	chr9:104165200-104172200	ZNF genes & repeats	GM12878-XiMat	blood
40	chr9:104165200-104172200	ZNF genes & repeats	K562	blood
41	chr9:104165200-104172600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
42	chr9:104165200-104172800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:104165400-104172000	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr9:104165400-104172000	ZNF genes & repeats	Fetal Kidney	kidney
45	chr9:104165400-104172200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
46	chr9:104165400-104172400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:104165400-104172400	ZNF genes & repeats	Fetal Muscle Trunk	muscle
48	chr9:104165400-104172600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
49	chr9:104165400-104172600	ZNF genes & repeats	Fetal Brain Female	brain
50	chr9:104165400-104172600	ZNF genes & repeats	Stomach Smooth Muscle	stomach

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