Variant report

Variant	rs1038092
Chromosome Location	chr9:97802593-97802594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97801094..97803225-chr9:97809368..97812078,2	K562	blood:
2	chr9:97800986..97803575-chr9:97807961..97810868,3	K562	blood:
3	chr9:97802158..97803981-chr9:97806425..97808316,2	K562	blood:
4	chr9:97794089..97795756-chr9:97801437..97804399,2	K562	blood:
5	chr9:97799572..97803967-chr9:97808050..97811094,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10761371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993471	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12555128	1.00[ASW][hapmap];1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.85[CHB][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1871220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	1.00[CEU][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs2061801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356685	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3739748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.86[MEX][hapmap];0.90[AMR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs475413	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs6479578	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs6479589	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs6479596	0.91[EUR][1000 genomes]
rs6479597	0.91[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7022963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750359	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750367	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72750373	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97789000-97806200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
4	chr9:97794200-97805800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:97794400-97806000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:97794600-97805000	Weak transcription	Fetal Thymus	thymus
8	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:97795200-97804000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr9:97795400-97803000	Enhancers	Colon Smooth Muscle	Colon
11	chr9:97795400-97806200	Genic enhancers	A549	lung
12	chr9:97795600-97806000	Weak transcription	Lung	lung
13	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:97797000-97807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:97798200-97804400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:97799000-97803200	Genic enhancers	Left Ventricle	heart
18	chr9:97799400-97807600	Weak transcription	Thymus	Thymus
19	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:97799600-97802800	Strong transcription	Hela-S3	cervix
21	chr9:97799800-97805400	Enhancers	Brain Cingulate Gyrus	brain
22	chr9:97799800-97806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:97800000-97808600	Genic enhancers	Liver	Liver
24	chr9:97800200-97802600	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr9:97800200-97806200	Strong transcription	Osteobl	bone
26	chr9:97800400-97802600	Weak transcription	Ovary	ovary
27	chr9:97800400-97802800	Strong transcription	Fetal Stomach	stomach
28	chr9:97800400-97806000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr9:97800400-97806000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:97800600-97804200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:97800600-97805600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr9:97800600-97806000	Weak transcription	Adipose Nuclei	Adipose
33	chr9:97800800-97803200	Genic enhancers	Fetal Muscle Leg	muscle
34	chr9:97800800-97804200	Genic enhancers	HepG2	liver
35	chr9:97801000-97802800	Weak transcription	Fetal Lung	lung
36	chr9:97801200-97802600	Weak transcription	Gastric	stomach
37	chr9:97801200-97802800	Weak transcription	Stomach Mucosa	stomach
38	chr9:97801200-97803000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr9:97801200-97803400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:97801200-97805400	Enhancers	Brain Substantia Nigra	brain
41	chr9:97801200-97806200	Weak transcription	NHDF-Ad	bronchial
42	chr9:97801400-97803200	Enhancers	Psoas Muscle	Psoas
43	chr9:97801400-97803400	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr9:97801400-97803600	Weak transcription	NH-A	brain
45	chr9:97801400-97805200	Enhancers	Brain Hippocampus Middle	brain
46	chr9:97801400-97806200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr9:97801400-97807000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr9:97801600-97802600	Weak transcription	Pancreas	Pancrea
49	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:97801800-97802600	Weak transcription	Placenta	Placenta

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