Variant report

Variant	rs4977492
Chromosome Location	chr9:19057551-19057552
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:19049339..19052176-chr9:19056143..19057826,3	MCF-7	breast:
2	chr9:19048116..19054448-chr9:19056568..19061765,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10122990	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10123400	0.88[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10123520	0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs10123624	0.89[ASW][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.85[ASN][1000 genomes]
rs10125646	0.83[ASW][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10125677	0.87[ASN][1000 genomes]
rs1048169	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10757024	0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10757025	0.85[ASN][1000 genomes]
rs10811103	0.81[ASN][1000 genomes]
rs10811104	0.85[ASN][1000 genomes]
rs10811107	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10811108	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs10811110	0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10963921	0.84[ASN][1000 genomes]
rs10963924	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs10963925	0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs10963942	0.94[ASW][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.81[MKK][hapmap];0.87[YRI][hapmap]
rs11515236	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs1154672	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1154673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12164262	0.84[ASN][1000 genomes]
rs12236347	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs12343169	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12380322	0.88[AFR][1000 genomes]
rs13287117	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13287517	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1932457	0.89[ASW][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[ASN][1000 genomes]
rs2130570	0.90[ASN][1000 genomes]
rs2130571	0.88[ASN][1000 genomes]
rs2233798	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35133951	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4392990	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4394488	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4439216	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4977278	0.85[ASN][1000 genomes]
rs4977490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62563593	0.84[AFR][1000 genomes]
rs62563594	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6475311	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6475312	0.85[ASN][1000 genomes]
rs6475313	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6475314	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475315	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68092871	0.84[ASN][1000 genomes]
rs7022576	0.88[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[YRI][hapmap]
rs7022807	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7027346	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035738	0.84[ASN][1000 genomes]
rs7036118	0.84[ASN][1000 genomes]
rs7036182	0.84[ASN][1000 genomes]
rs7036301	0.84[ASN][1000 genomes]
rs7037772	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7037787	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7043115	0.85[ASN][1000 genomes]
rs7043507	0.85[ASN][1000 genomes]
rs7045844	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7467137	0.84[JPT][hapmap]
rs7467618	0.88[ASW][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7854858	0.93[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7854974	0.85[ASN][1000 genomes]
rs7855250	0.84[ASN][1000 genomes]
rs7855338	0.81[ASN][1000 genomes]
rs7856768	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7859259	0.93[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs9298795	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	esv3408862	chr9:19056310-19058050	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4977492	RRAGA	cis	cerebellum	SCAN
rs4977492	FAM29A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:19050600-19060800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:19050600-19062600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:19050600-19063600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:19050600-19069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:19050800-19074200	Weak transcription	Lung	lung
6	chr9:19051000-19059000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:19051400-19066400	Weak transcription	Colonic Mucosa	Colon
8	chr9:19051600-19074400	Weak transcription	Spleen	Spleen
9	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:19051800-19059000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr9:19051800-19059400	Weak transcription	HSMMtube	muscle
12	chr9:19051800-19070200	Weak transcription	Fetal Kidney	kidney
13	chr9:19051800-19089000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:19052000-19057800	Weak transcription	NHLF	lung
15	chr9:19052000-19059000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:19052000-19061800	Weak transcription	Stomach Mucosa	stomach
17	chr9:19052000-19062600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:19052000-19075200	Weak transcription	Right Ventricle	heart
19	chr9:19052400-19077000	Weak transcription	Pancreas	Pancrea
20	chr9:19052600-19057800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:19052600-19059200	Weak transcription	Brain Anterior Caudate	brain
22	chr9:19052600-19065000	Weak transcription	Small Intestine	intestine
23	chr9:19052800-19059200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:19052800-19059200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr9:19052800-19061600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr9:19052800-19062600	Weak transcription	Brain Angular Gyrus	brain
27	chr9:19052800-19074400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:19052800-19075600	Weak transcription	Aorta	Aorta
29	chr9:19052800-19092400	Weak transcription	Fetal Brain Male	brain
30	chr9:19053400-19059400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:19053600-19065000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:19054400-19097800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr9:19054800-19098200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:19054800-19100800	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:19055000-19072600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:19055200-19065600	Strong transcription	Placenta	Placenta
37	chr9:19055400-19065600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr9:19055400-19065600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:19055600-19082600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:19055600-19091200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr9:19055800-19065400	Strong transcription	Dnd41	blood
42	chr9:19055800-19065400	Strong transcription	HUVEC	blood vessel
43	chr9:19055800-19079800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:19055800-19085200	Strong transcription	Liver	Liver
45	chr9:19055800-19096800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:19055800-19098200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr9:19056000-19058400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:19056000-19058400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr9:19056000-19086000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr9:19056000-19091200	Strong transcription	Primary monocytes fromperipheralblood	blood

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