Variant report

Variant	rs2272785
Chromosome Location	chr1:175161599-175161600
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:175161040..175161921-chr7:112091025..112091650,2	Hela-S3	cervix:
2	chr1:175160599..175162642-chr17:57913163..57915904,2	MCF-7	breast:
3	chr1:175161160..175161875-chr4:120988169..120988671,2	Hela-S3	cervix:
4	chr1:175160152..175162627-chr1:176175775..176178430,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006652	Chromatin interaction
ENSG00000250938	Chromatin interaction
ENSG00000164109	Chromatin interaction
ENSG00000236021	Chromatin interaction
ENSG00000143207	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1008459	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136973	1.00[ASW][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs2205604	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861158	1.00[ASW][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap]
rs3753559	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753560	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766686	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766690	1.00[ASW][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs3766691	0.81[CHB][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap]
rs3766695	0.81[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap]
rs760486	0.83[MEX][hapmap]

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	nsv949473	chr1:175151666-175391741	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2272785	SNORD79	cis	parietal	SCAN
rs2272785	FMO1	cis	cerebellum	SCAN
rs2272785	KIAA0040	cis	lymphoblastoid	seeQTL
rs2272785	KIAA0040	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175157600-175161600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:175157800-175161600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr1:175158400-175161800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:175158400-175162800	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:175159200-175162600	Active TSS	Lung	lung
6	chr1:175159600-175161800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr1:175159600-175161800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:175159800-175162600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:175160000-175161800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:175160400-175162200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr1:175160400-175162200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:175160400-175162200	Active TSS	GM12878-XiMat	blood
13	chr1:175160400-175162400	Active TSS	Colonic Mucosa	Colon
14	chr1:175160400-175162400	Active TSS	Pancreas	Pancrea
15	chr1:175160400-175162600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr1:175160600-175161800	Active TSS	Stomach Mucosa	stomach
17	chr1:175160600-175161800	Flanking Bivalent TSS/Enh	Dnd41	blood
18	chr1:175160600-175162200	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr1:175160600-175162400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr1:175160600-175162400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:175160600-175162400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr1:175160600-175163000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:175160600-175163200	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:175160800-175161600	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:175160800-175161600	Flanking Bivalent TSS/Enh	HepG2	liver
26	chr1:175160800-175161800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
27	chr1:175160800-175162200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:175160800-175162200	Active TSS	Primary B cells from peripheral blood	blood
29	chr1:175160800-175162200	Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:175160800-175162200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:175160800-175162200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr1:175160800-175162200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:175160800-175162200	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr1:175160800-175162200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:175160800-175162200	Active TSS	HMEC	breast
36	chr1:175160800-175162200	Active TSS	NHEK	skin
37	chr1:175160800-175162400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:175160800-175162400	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr1:175160800-175162400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:175160800-175162400	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr1:175160800-175162400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:175160800-175162400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr1:175160800-175162400	Active TSS	Esophagus	oesophagus
44	chr1:175160800-175162400	Active TSS	Fetal Muscle Trunk	muscle
45	chr1:175160800-175162400	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:175160800-175162400	Active TSS	Right Atrium	heart
47	chr1:175160800-175162400	Active TSS	Right Ventricle	heart
48	chr1:175160800-175162400	Active TSS	Small Intestine	intestine
49	chr1:175160800-175162600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
50	chr1:175160800-175162600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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