Variant report

Variant	rs2274914
Chromosome Location	chr9:86500979-86500980
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	chr9:86499637..86502408-chr9:86534472..86537007,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10116542	0.92[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap]
rs10125556	0.89[CHB][hapmap]
rs10453251	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs10746724	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs10780628	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs10780631	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs10780633	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs10868046	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs10868047	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs10868048	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs10868052	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs10868053	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap]
rs10868054	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs10868057	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs10868060	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs10868061	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs10868062	0.96[CEU][hapmap];0.88[CHB][hapmap]
rs10868063	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs11140237	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs11140242	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs11140243	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs11140247	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs12057022	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs12057070	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs12339076	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs12344567	0.95[CEU][hapmap];0.94[CHB][hapmap]
rs1558922	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs1582396	0.88[CEU][hapmap];0.89[CHB][hapmap]
rs1831758	1.00[CEU][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2098494	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs2111683	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2160821	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs2287373	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.98[TSI][hapmap]
rs295269	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs295271	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs295272	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs295276	0.96[CEU][hapmap]
rs295280	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs295283	0.92[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs295293	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs3763622	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs4242624	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs4298563	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4348579	0.95[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs4750	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs4877265	0.96[CEU][hapmap]
rs4877809	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs4877810	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs4877811	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs62565774	0.85[EUR][1000 genomes]
rs7021357	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs7031676	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]
rs7036960	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7042776	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs7044691	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs7859179	0.92[CEU][hapmap];0.98[GIH][hapmap];0.93[TSI][hapmap]
rs7864189	0.92[CEU][hapmap];0.89[CHB][hapmap]
rs918223	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	esv2753071	chr9:86500946-86517546	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2274914	LOC440173	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
2	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
3	chr9:86461600-86535400	Weak transcription	Ovary	ovary
4	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
5	chr9:86462600-86503800	Weak transcription	Dnd41	blood
6	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
7	chr9:86462800-86515000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:86462800-86518000	Weak transcription	Fetal Intestine Large	intestine
9	chr9:86462800-86518000	Weak transcription	Fetal Stomach	stomach
10	chr9:86481000-86535800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:86482000-86518000	Weak transcription	Left Ventricle	heart
12	chr9:86490400-86510800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:86491000-86535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr9:86491200-86502200	Weak transcription	Brain Germinal Matrix	brain
15	chr9:86491200-86535200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr9:86491400-86518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr9:86491800-86518200	Weak transcription	Primary B cells from cord blood	blood
18	chr9:86495000-86518000	Weak transcription	Primary T cells from cord blood	blood
19	chr9:86496000-86535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:86496400-86533000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:86496600-86515600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:86498800-86504000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:86499200-86513400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:86499400-86501600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:86499400-86518200	Weak transcription	Fetal Muscle Leg	muscle
26	chr9:86499400-86535000	Weak transcription	Fetal Kidney	kidney
27	chr9:86499800-86501400	Enhancers	HUVEC	blood vessel
28	chr9:86499800-86501800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr9:86499800-86501800	Enhancers	HMEC	breast
30	chr9:86499800-86523200	Weak transcription	Fetal Thymus	thymus
31	chr9:86500000-86501400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr9:86500000-86501800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:86500000-86501800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:86500000-86534800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr9:86500200-86501200	Enhancers	NH-A	brain
36	chr9:86500200-86501400	Enhancers	A549	lung
37	chr9:86500200-86501800	Enhancers	NHEK	skin
38	chr9:86500200-86521200	Weak transcription	Adipose Nuclei	Adipose
39	chr9:86500200-86521200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:86500200-86535200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:86500200-86535200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr9:86500200-86535600	Weak transcription	Lung	lung
43	chr9:86500400-86501800	Enhancers	Hela-S3	cervix
44	chr9:86500600-86501800	Strong transcription	Fetal Lung	lung
45	chr9:86500600-86502000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:86500600-86503000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:86500800-86501000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:86500800-86501200	Enhancers	HepG2	liver
49	chr9:86500800-86501400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr9:86500800-86501600	Enhancers	Osteobl	bone

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