Variant report

Variant	rs9288163
Chromosome Location	chr2:190013146-190013147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190010189..190015498-chr2:190084856..190090227,6	MCF-7	breast:
2	chr2:190012942..190018195-chr2:190085147..190088368,4	MCF-7	breast:
3	chr2:190012335..190014833-chr2:190305566..190308252,2	K562	blood:
4	chr2:190011309..190014664-chr2:190015340..190018196,3	MCF-7	breast:
5	chr2:190011437..190014058-chr2:190146066..190148216,2	MCF-7	breast:
6	chr2:190006464..190008527-chr2:190011142..190013874,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10165127	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10165257	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1016622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10166385	0.81[AFR][1000 genomes]
rs10931401	1.00[CEU][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.92[EUR][1000 genomes]
rs10931411	0.82[EUR][1000 genomes]
rs11901914	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12474942	0.88[AFR][1000 genomes]
rs12618316	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005714	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005834	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13006065	0.92[EUR][1000 genomes]
rs13013089	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13019651	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13020999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13024858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13030984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1464135	1.00[CEU][hapmap];0.83[JPT][hapmap];0.92[EUR][1000 genomes]
rs1515864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1515869	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1533618	0.88[EUR][1000 genomes]
rs1949327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2138373	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36019389	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4417749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667263	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4667268	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4667270	0.88[AFR][1000 genomes]
rs4667271	0.88[EUR][1000 genomes]
rs4667275	0.82[EUR][1000 genomes]
rs62182417	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6434324	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6434325	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6730236	0.92[CHB][hapmap]
rs6741804	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6749559	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7560973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7593860	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7599222	0.88[EUR][1000 genomes]
rs7606337	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9288163	AC013439.4	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189981400-190014800	Weak transcription	Fetal Stomach	stomach
2	chr2:189984000-190016800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:189993800-190017000	Weak transcription	Ovary	ovary
4	chr2:190000400-190013600	Weak transcription	Left Ventricle	heart
5	chr2:190003600-190014600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:190008000-190014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:190009000-190016000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:190009200-190014400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:190009400-190014800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr2:190009600-190013200	Genic enhancers	Osteobl	bone
11	chr2:190009600-190014800	Weak transcription	Aorta	Aorta
12	chr2:190009800-190013800	Weak transcription	Adipose Nuclei	Adipose
13	chr2:190009800-190014600	Weak transcription	NH-A	brain
14	chr2:190009800-190017200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:190010200-190013200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:190010200-190013800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:190011000-190014800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:190011200-190020800	Enhancers	NHDF-Ad	bronchial
19	chr2:190011600-190016200	Weak transcription	Fetal Lung	lung
20	chr2:190012000-190013200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:190012000-190013600	Genic enhancers	A549	lung
22	chr2:190012000-190014600	Weak transcription	NHLF	lung
23	chr2:190012200-190013200	Strong transcription	HSMM	muscle
24	chr2:190012200-190013600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:190012200-190016800	Weak transcription	HSMMtube	muscle
26	chr2:190012400-190013800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:190012400-190014000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:190012400-190018000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:190012600-190013800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr2:190012600-190017200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:190013000-190013200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:190013000-190014200	Weak transcription	Muscle Satellite Cultured Cells	--

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