Variant report

Variant	rs9289981
Chromosome Location	chr3:99868104-99868105
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99866434..99868152-chr3:99908840..99911443,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10222474	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487143	1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs12488245	0.91[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12629505	0.82[ASN][1000 genomes]
rs13059754	0.87[CEU][hapmap]
rs1387647	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2130369	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2316263	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs4928150	0.87[CEU][hapmap]
rs4928151	0.84[CEU][hapmap]
rs4928153	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4928237	0.84[CEU][hapmap]
rs6440967	0.87[CEU][hapmap]
rs6767441	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798114	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6802817	0.87[CEU][hapmap]
rs6806323	0.87[CEU][hapmap]
rs720688	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7619080	0.84[ASN][1000 genomes]
rs7629487	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636776	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649349	0.87[CEU][hapmap]
rs766778	0.87[CEU][hapmap]
rs902159	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs923472	0.84[CEU][hapmap]
rs9811920	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	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837131	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849632	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865713	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9289981	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99847000-99868800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:99856000-99877800	Weak transcription	Ovary	ovary
3	chr3:99858600-99868600	Weak transcription	Pancreas	Pancrea
4	chr3:99858600-99877200	Weak transcription	HSMM	muscle
5	chr3:99859200-99870200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:99860200-99874000	Weak transcription	A549	lung
7	chr3:99860800-99868400	Weak transcription	NHDF-Ad	bronchial
8	chr3:99861000-99870000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:99861600-99870400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:99862000-99868200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:99862200-99874200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:99862800-99870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:99863400-99872200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:99863400-99873800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:99863400-99874000	Weak transcription	NHEK	skin
16	chr3:99863600-99868600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:99863600-99874000	Weak transcription	GM12878-XiMat	blood
18	chr3:99863800-99873000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:99863800-99873600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr3:99863800-99874000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:99864000-99873400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:99864400-99886600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:99864600-99870800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:99864600-99873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:99864800-99869000	Weak transcription	Fetal Lung	lung
26	chr3:99865000-99873400	Weak transcription	Fetal Intestine Small	intestine
27	chr3:99865000-99894600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:99865400-99873800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:99865600-99898400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:99865800-99868600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:99866000-99869000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:99866000-99874000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:99866400-99868400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:99866400-99871200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:99866400-99874200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:99866600-99870000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:99866600-99870200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:99866600-99871400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:99866600-99872600	Strong transcription	Primary T cells from cord blood	blood
40	chr3:99866800-99868400	Weak transcription	Thymus	Thymus
41	chr3:99866800-99870000	Weak transcription	Brain Anterior Caudate	brain
42	chr3:99867000-99868600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:99867000-99868600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:99867000-99870000	Weak transcription	HSMMtube	muscle
45	chr3:99867200-99868400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:99867200-99874000	Weak transcription	K562	blood
47	chr3:99867400-99874000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:99867600-99874000	Weak transcription	Dnd41	blood
49	chr3:99867800-99869000	Enhancers	Stomach Mucosa	stomach
50	chr3:99868000-99868200	Enhancers	Duodenum Mucosa	Duodenum

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