Variant report

Variant	rs12338859
Chromosome Location	chr9:97663620-97663621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97655373..97657795-chr9:97662890..97664945,2	MCF-7	breast:
2	chr9:97629113..97631715-chr9:97662982..97664521,2	MCF-7	breast:
3	chr9:97663421..97665287-chr9:97685547..97688142,2	MCF-7	breast:
4	chr9:97663154..97665025-chr9:97680451..97683627,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10081676	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10217143	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10761361	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821392	0.91[YRI][hapmap]
rs10821398	0.81[CEU][hapmap];0.95[YRI][hapmap]
rs10821404	0.80[AFR][1000 genomes]
rs10821410	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10821413	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10993387	0.93[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12338409	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12344211	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12347649	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1867102	0.94[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4743969	0.94[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4743974	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4744386	0.94[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs4744412	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7027708	0.91[YRI][hapmap]
rs7847277	0.88[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs7848139	0.88[ASW][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap]
rs7862219	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7870160	0.85[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9802263	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97633400-97671800	Weak transcription	Esophagus	oesophagus
2	chr9:97655800-97668400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:97656400-97669000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:97657000-97663800	Weak transcription	Stomach Mucosa	stomach
5	chr9:97658800-97668400	Weak transcription	Pancreas	Pancrea
6	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
7	chr9:97661000-97666000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
9	chr9:97661800-97665200	Flanking Active TSS	A549	lung
10	chr9:97662200-97663800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr9:97662200-97663800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr9:97662200-97665200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr9:97662400-97663800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:97662400-97664200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr9:97662400-97664200	Enhancers	Fetal Brain Male	brain
16	chr9:97662400-97664800	Enhancers	Brain Angular Gyrus	brain
17	chr9:97662400-97664800	Enhancers	Brain Cingulate Gyrus	brain
18	chr9:97662400-97665000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr9:97662400-97665000	Enhancers	HMEC	breast
20	chr9:97662400-97665200	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr9:97662400-97665600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:97662400-97666200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:97662400-97678600	Enhancers	Brain Substantia Nigra	brain
24	chr9:97662600-97664000	Weak transcription	Psoas Muscle	Psoas
25	chr9:97662600-97669600	Weak transcription	Right Atrium	heart
26	chr9:97662600-97670000	Weak transcription	Fetal Intestine Small	intestine
27	chr9:97662600-97680400	Enhancers	Brain Hippocampus Middle	brain
28	chr9:97662800-97663800	Weak transcription	Placenta	Placenta
29	chr9:97662800-97664200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:97662800-97664800	Enhancers	Rectal Smooth Muscle	rectum
31	chr9:97662800-97665400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr9:97662800-97669200	Weak transcription	Lung	lung
33	chr9:97662800-97670000	Weak transcription	Fetal Intestine Large	intestine
34	chr9:97663000-97663800	Enhancers	Adipose Nuclei	Adipose
35	chr9:97663000-97664400	Enhancers	Colon Smooth Muscle	Colon
36	chr9:97663200-97664200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:97663200-97664200	Weak transcription	Brain Anterior Caudate	brain
38	chr9:97663200-97664200	Enhancers	HSMM	muscle
39	chr9:97663200-97664400	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:97663200-97664400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:97663200-97664800	Enhancers	Ovary	ovary
42	chr9:97663200-97664800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr9:97663200-97665000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:97663200-97665200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:97663200-97665400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:97663200-97666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:97663400-97663800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:97663400-97664400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr9:97663400-97664800	Enhancers	NH-A	brain
50	chr9:97663400-97665000	Enhancers	Pancreatic Islets	Pancreatic Islet

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