Variant report

Variant	rs906487
Chromosome Location	chr4:48049654-48049655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48040732..48041262-chr4:48049418..48050146,3	MCF-7	breast:
2	chr4:48040732..48041255-chr4:48049418..48050146,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10517204	0.87[JPT][hapmap]
rs10805163	0.87[JPT][hapmap]
rs13107767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1396051	0.87[JPT][hapmap]
rs1507925	0.83[ASN][1000 genomes]
rs2230594	0.81[ASN][1000 genomes]
rs28650378	0.80[ASN][1000 genomes]
rs28667740	0.82[ASN][1000 genomes]
rs33964061	0.81[ASN][1000 genomes]
rs3805187	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs4340770	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4694880	0.87[JPT][hapmap]
rs4695332	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6447610	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447611	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447612	0.80[ASN][1000 genomes]
rs6447613	0.80[ASN][1000 genomes]
rs6447614	0.81[ASN][1000 genomes]
rs6829490	0.80[ASN][1000 genomes]
rs6839501	0.80[ASN][1000 genomes]
rs9996535	0.91[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs906487	CNGA1	cis	Adipose Subcutaneous	GTEx
rs906487	CNGA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
2	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:48041600-48053000	Weak transcription	HMEC	breast
4	chr4:48045400-48052200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:48045800-48052600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48046400-48050400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr4:48048000-48050400	Enhancers	Fetal Thymus	thymus
8	chr4:48048200-48050400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr4:48048200-48050600	Enhancers	Primary hematopoietic stem cells	blood
10	chr4:48048200-48051400	Enhancers	Fetal Heart	heart
11	chr4:48048400-48050400	Enhancers	Small Intestine	intestine
12	chr4:48048600-48050200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
13	chr4:48048600-48050400	Enhancers	Stomach Mucosa	stomach
14	chr4:48048600-48051200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr4:48048800-48049800	Weak transcription	Psoas Muscle	Psoas
16	chr4:48048800-48050600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr4:48049000-48049800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr4:48049000-48050000	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr4:48049000-48050200	Enhancers	Thymus	Thymus
20	chr4:48049000-48050400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr4:48049000-48050600	Enhancers	Liver	Liver
22	chr4:48049000-48050600	Flanking Active TSS	GM12878-XiMat	blood
23	chr4:48049000-48051000	Enhancers	Primary B cells from peripheral blood	blood
24	chr4:48049200-48049800	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr4:48049200-48049800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr4:48049200-48049800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr4:48049200-48050000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:48049200-48050000	Enhancers	Dnd41	blood
29	chr4:48049200-48050200	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr4:48049200-48050200	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr4:48049200-48050200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:48049400-48049800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr4:48049400-48049800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
34	chr4:48049400-48049800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr4:48049400-48049800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:48049400-48049800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr4:48049400-48050000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr4:48049400-48050200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:48049400-48050200	Enhancers	Right Atrium	heart
40	chr4:48049400-48050200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:48049400-48051800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:48049600-48049800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:48049600-48049800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
44	chr4:48049600-48049800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr4:48049600-48049800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:48049600-48049800	Enhancers	Fetal Muscle Trunk	muscle
47	chr4:48049600-48049800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr4:48049600-48050000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:48049600-48050000	Bivalent Enhancer	Adipose Nuclei	Adipose
50	chr4:48049600-48050000	Enhancers	Colonic Mucosa	Colon

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