Variant report

Variant	rs12343530
Chromosome Location	chr9:97532193-97532194
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97520861..97523469-chr9:97531163..97533189,3	MCF-7	breast:
2	chr9:97529861..97533578-chr9:97534032..97536715,3	K562	blood:
3	chr9:97529221..97532775-chr9:97533309..97537011,4	K562	blood:
4	chr9:97530626..97534561-chr9:97683586..97686603,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10122127	1.00[JPT][hapmap]
rs1028843	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10512234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10732405	1.00[JPT][hapmap]
rs10993325	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10993329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993337	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993341	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993349	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993350	0.81[EUR][1000 genomes]
rs10993351	1.00[JPT][hapmap]
rs10993360	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10993362	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10993363	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993364	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10993381	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs10993391	1.00[TSI][hapmap]
rs12336061	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12336437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12337706	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]
rs12337992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12338982	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344052	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs12344157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12344256	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12345098	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12345321	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12345783	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12346548	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12348060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12348206	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12351111	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12352600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12352856	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911670	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16911713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2025793	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304884	1.00[JPT][hapmap]
rs242259	1.00[JPT][hapmap]
rs34335636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356135	1.00[JPT][hapmap]
rs376902	1.00[JPT][hapmap]
rs3808890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858088	1.00[JPT][hapmap]
rs41281168	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4744380	1.00[JPT][hapmap]
rs60048957	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60514919	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61446634	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7031172	1.00[JPT][hapmap]
rs7045387	1.00[JPT][hapmap]
rs7866487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7869666	1.00[JPT][hapmap]
rs925813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9987493	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9987549	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9987803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1041922	chr9:97444976-97536753	Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97506200-97533400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr9:97509200-97536000	Weak transcription	Pancreas	Pancrea
3	chr9:97512600-97540800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr9:97512600-97544600	Weak transcription	Psoas Muscle	Psoas
5	chr9:97519800-97544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:97521800-97541200	Weak transcription	Right Ventricle	heart
7	chr9:97522400-97540400	Weak transcription	Fetal Heart	heart
8	chr9:97522800-97532600	Weak transcription	K562	blood
9	chr9:97522800-97534600	Weak transcription	Fetal Brain Male	brain
10	chr9:97522800-97534600	Weak transcription	NHLF	lung
11	chr9:97523000-97534600	Weak transcription	Ovary	ovary
12	chr9:97523200-97532600	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:97523200-97535000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:97523400-97533000	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:97523400-97533400	Weak transcription	Brain Substantia Nigra	brain
16	chr9:97523400-97533600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:97523400-97534400	Weak transcription	Osteobl	bone
18	chr9:97523400-97534600	Weak transcription	Right Atrium	heart
19	chr9:97523400-97535600	Weak transcription	Aorta	Aorta
20	chr9:97523400-97535800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr9:97523400-97541400	Weak transcription	NHEK	skin
22	chr9:97523400-97544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:97523400-97544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr9:97523400-97545200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:97523400-97545200	Weak transcription	Liver	Liver
26	chr9:97523400-97545200	Weak transcription	Lung	lung
27	chr9:97523400-97545400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:97523400-97552600	Weak transcription	Dnd41	blood
29	chr9:97523400-97554000	Weak transcription	Primary T cells from cord blood	blood
30	chr9:97523400-97557800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:97523400-97563800	Weak transcription	Fetal Kidney	kidney
32	chr9:97523600-97532200	Weak transcription	Fetal Intestine Small	intestine
33	chr9:97523600-97533600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:97523600-97534600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:97523600-97534600	Weak transcription	HSMM	muscle
36	chr9:97523600-97534600	Weak transcription	HSMMtube	muscle
37	chr9:97523600-97535200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:97523600-97535200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr9:97523600-97535600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr9:97523600-97535800	Weak transcription	HepG2	liver
41	chr9:97523600-97536000	Weak transcription	Spleen	Spleen
42	chr9:97523600-97540400	Weak transcription	A549	lung
43	chr9:97523600-97545000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr9:97523600-97545200	Weak transcription	Left Ventricle	heart
45	chr9:97523600-97549400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:97523600-97552600	Weak transcription	Thymus	Thymus
47	chr9:97523600-97554400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr9:97523800-97544200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr9:97524000-97534000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr9:97524000-97534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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