Variant report

Variant	rs9811920
Chromosome Location	chr3:99844293-99844294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99822715..99823609-chr3:99844082..99845045,5	MCF-7	breast:
2	chr3:99822635..99823609-chr3:99844048..99844892,9	MCF-7	breast:
3	chr3:99829489..99831303-chr3:99842573..99844567,2	K562	blood:
4	chr3:99843535..99846407-chr3:99848522..99850421,2	K562	blood:
5	chr3:99832676..99835044-chr3:99842205..99844434,2	MCF-7	breast:
6	chr3:99840756..99842324-chr3:99842654..99845217,2	K562	blood:

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10222474	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487143	1.00[CHB][hapmap]
rs12488245	0.96[CEU][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13059754	0.92[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap]
rs1387647	0.92[CEU][hapmap];0.85[GIH][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2130369	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2316263	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[MKK][hapmap]
rs4577503	0.92[CEU][hapmap];0.85[GIH][hapmap];0.83[LWK][hapmap]
rs4928150	0.92[CEU][hapmap];0.82[GIH][hapmap]
rs4928151	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4928153	0.83[ASW][hapmap];0.92[CEU][hapmap];0.85[GIH][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4928237	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6440967	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs6767441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6798114	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6802817	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6806323	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs6808765	0.81[EUR][1000 genomes]
rs720688	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7636776	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649349	0.92[CEU][hapmap];0.85[GIH][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs766778	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs902159	0.92[CEU][hapmap];0.80[GIH][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923472	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs9289981	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837131	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849632	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865713	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Axial length	24144296	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9811920	OR5H6	cis	cerebellum	SCAN
rs9811920	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:99840400-99844600	Enhancers	Fetal Muscle Leg	muscle
4	chr3:99841200-99846000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:99841200-99846800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:99842000-99844600	Enhancers	Psoas Muscle	Psoas
7	chr3:99842200-99844800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:99842400-99844400	Enhancers	Fetal Heart	heart
9	chr3:99842400-99845200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:99842600-99845000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:99843200-99844400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr3:99843200-99844600	Enhancers	Fetal Stomach	stomach
13	chr3:99843200-99844600	Enhancers	Spleen	Spleen
14	chr3:99843600-99844400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:99843600-99844400	Enhancers	HUVEC	blood vessel
16	chr3:99843800-99844800	Enhancers	Stomach Smooth Muscle	stomach
17	chr3:99843800-99846000	Weak transcription	Left Ventricle	heart
18	chr3:99843800-99855200	Weak transcription	Ovary	ovary
19	chr3:99844000-99844400	Enhancers	Fetal Kidney	kidney
20	chr3:99844000-99844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:99844000-99844600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:99844000-99844600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:99844000-99844600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:99844000-99844600	Enhancers	Small Intestine	intestine
25	chr3:99844000-99844800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:99844000-99854200	Weak transcription	Right Atrium	heart
27	chr3:99844200-99844600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:99844200-99844600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:99844200-99844600	Enhancers	Primary hematopoietic stem cells	blood
30	chr3:99844200-99844600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr3:99844200-99844600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:99844200-99844600	Enhancers	NH-A	brain
33	chr3:99844200-99845000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:99844200-99845200	Enhancers	Colon Smooth Muscle	Colon
35	chr3:99844200-99846200	Weak transcription	Right Ventricle	heart

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