Variant report

Variant	rs12336513
Chromosome Location	chr9:101945827-101945828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:101945788..101948395-chr9:101983472..101985266,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106803	Chromatin interaction
ENSG00000119523	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10114715	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10121020	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs10819641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10988738	0.87[YRI][hapmap]
rs10988740	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10988742	0.85[ASW][hapmap];0.87[YRI][hapmap]
rs10988743	0.82[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988745	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes]
rs10988746	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10988749	1.00[CEU][hapmap]
rs12336759	0.87[YRI][hapmap]
rs12336790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12340839	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs12340952	0.83[YRI][hapmap]
rs12345762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13440104	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16905728	0.87[YRI][hapmap]
rs16918352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2221383	0.85[ASW][hapmap];0.87[YRI][hapmap]
rs57839076	0.84[AFR][1000 genomes]
rs59091994	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6478976	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes]
rs7022989	0.86[JPT][hapmap]
rs7872043	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs912248	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs912249	1.00[CEU][hapmap];0.96[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	nsv831666	chr9:101874985-102018690	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101931600-101947000	Weak transcription	Right Atrium	heart
2	chr9:101935200-101947200	Weak transcription	Gastric	stomach
3	chr9:101936600-101949600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr9:101939200-101946400	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr9:101941800-101946800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr9:101942200-101946800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:101943400-101946000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:101943400-101946400	Weak transcription	Fetal Stomach	stomach
9	chr9:101943800-101946400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr9:101943800-101946800	Weak transcription	Fetal Intestine Large	intestine
11	chr9:101944200-101946800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr9:101944200-101947200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:101944400-101946400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr9:101944400-101946400	Weak transcription	NH-A	brain
15	chr9:101944400-101946800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:101944400-101946800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr9:101944400-101946800	Weak transcription	Thymus	Thymus
18	chr9:101944600-101946400	Weak transcription	Colonic Mucosa	Colon
19	chr9:101944600-101946800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr9:101944600-101949000	Enhancers	GM12878-XiMat	blood
21	chr9:101944800-101946200	Weak transcription	HSMM	muscle
22	chr9:101944800-101946400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr9:101944800-101946400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:101945000-101946400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr9:101945000-101946800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:101945000-101946800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr9:101945000-101946800	Weak transcription	Primary B cells from cord blood	blood
28	chr9:101945000-101946800	Weak transcription	Osteobl	bone
29	chr9:101945200-101946000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:101945400-101946400	Weak transcription	Fetal Lung	lung
31	chr9:101945400-101947000	Enhancers	Primary hematopoietic stem cells	blood
32	chr9:101945600-101946200	Enhancers	Primary T cells from cord blood	blood
33	chr9:101945600-101946800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr9:101945600-101946800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:101945600-101946800	Enhancers	Stomach Smooth Muscle	stomach
36	chr9:101945600-101947000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr9:101945800-101946000	Enhancers	Fetal Intestine Small	intestine
38	chr9:101945800-101946600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:101945800-101947000	Enhancers	Fetal Muscle Leg	muscle
40	chr9:101945800-101947400	Enhancers	Fetal Thymus	thymus
41	chr9:101945800-101947800	Enhancers	Primary hematopoietic stem cells short term culture	blood

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