Variant report

Variant	rs9425766
Chromosome Location	chr1:173853127-173853128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173834423..173839746-chr1:173850536..173854569,6	K562	blood:
2	chr1:173845893..173848745-chr1:173851379..173854012,4	K562	blood:
3	chr1:173846395..173848405-chr1:173851384..173853662,2	MCF-7	breast:
4	chr1:173853006..173854798-chr1:173856901..173859018,2	K562	blood:
5	chr1:173831191..173840458-chr1:173852193..173864862,18	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270084	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000185278	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10798295	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs10798301	0.91[CHB][hapmap];0.82[CHD][hapmap];0.80[JPT][hapmap]
rs10798302	0.87[CHB][hapmap]
rs10912676	0.80[AMR][1000 genomes]
rs12066153	0.87[CHB][hapmap]
rs12071594	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12071663	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078824	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322770	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322780	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1799876	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884994	0.83[CHB][hapmap]
rs1951627	0.87[CHB][hapmap];0.87[GIH][hapmap];0.83[MKK][hapmap]
rs2065171	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295366	0.84[MEX][hapmap]
rs4652229	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5877	0.85[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5878	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663875	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665484	0.87[CHB][hapmap]
rs6677660	0.87[CHB][hapmap]
rs6686083	0.87[CHB][hapmap]
rs6689285	0.87[CHB][hapmap]
rs6696163	0.87[CHB][hapmap]
rs714624	0.87[CHB][hapmap]
rs7349095	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7413166	0.86[CHB][hapmap]
rs7544605	0.86[AMR][1000 genomes]
rs7552939	0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9286895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941989	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9425430	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425435	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425755	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9425756	0.84[MEX][hapmap]
rs9425765	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9661233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9425766		cis	Lymphoblastoid	GTEx
rs9425766	FMO1	cis	cerebellum	SCAN
rs9425766	SNORD78	cis	parietal	SCAN
rs9425766	CENPL	cis	lymphoblastoid	seeQTL
rs9425766	DARS2	cis	cerebellum	SCAN
rs9425766	PRDX6	cis	parietal	SCAN
rs9425766	RABGAP1L	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173854200	Weak transcription	Gastric	stomach
2	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
3	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
4	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
5	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
6	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:173839000-173854800	Weak transcription	Colon Smooth Muscle	Colon
10	chr1:173839000-173862800	Weak transcription	HMEC	breast
11	chr1:173839200-173855000	Weak transcription	A549	lung
12	chr1:173839600-173854600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:173840200-173854200	Weak transcription	Colonic Mucosa	Colon
14	chr1:173840200-173854800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:173840400-173855000	Weak transcription	Psoas Muscle	Psoas
17	chr1:173840600-173854200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:173840800-173854200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:173840800-173854200	Weak transcription	Brain Anterior Caudate	brain
20	chr1:173840800-173854200	Weak transcription	NHLF	lung
21	chr1:173840800-173854600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:173840800-173854600	Weak transcription	Hela-S3	cervix
23	chr1:173840800-173854800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:173840800-173854800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:173840800-173855000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:173840800-173855000	Weak transcription	NHDF-Ad	bronchial
27	chr1:173841000-173854800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:173841000-173854800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:173841000-173864400	Weak transcription	Fetal Heart	heart
30	chr1:173841000-173868600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr1:173841200-173854800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:173841800-173854800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr1:173841800-173854800	Weak transcription	K562	blood
34	chr1:173842600-173855000	Weak transcription	GM12878-XiMat	blood
35	chr1:173842800-173855200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:173842800-173859200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:173843200-173854800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:173843200-173854800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:173845000-173854800	Weak transcription	Spleen	Spleen
40	chr1:173845200-173854200	Weak transcription	Left Ventricle	heart
41	chr1:173845200-173854200	Weak transcription	Lung	lung
42	chr1:173845200-173854800	Weak transcription	Ovary	ovary
43	chr1:173845200-173854800	Weak transcription	NHEK	skin
44	chr1:173845400-173853200	Weak transcription	Fetal Intestine Small	intestine
45	chr1:173845800-173854000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:173845800-173854200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:173845800-173854800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:173846000-173854800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr1:173846200-173854600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:173846200-173854800	Weak transcription	Thymus	Thymus

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