Variant report

Variant	rs12340531
Chromosome Location	chr9:5999374-5999375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:5995960..5997712-chr9:5997780..6000684,2	MCF-7	breast:
2	chr9:5997327..6003105-chr9:6004603..6008619,8	K562	blood:

Variant related genes	Relation type
ENSG00000183354	Chromatin interaction
ENSG00000263575	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10116214	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10975350	1.00[EUR][1000 genomes]
rs10975351	1.00[EUR][1000 genomes]
rs10975362	1.00[EUR][1000 genomes]
rs10975363	1.00[EUR][1000 genomes]
rs10975364	1.00[EUR][1000 genomes]
rs10975372	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10975377	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506678	1.00[EUR][1000 genomes]
rs11793956	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs12337300	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12337445	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12337790	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339713	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339886	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12340153	1.00[EUR][1000 genomes]
rs12341021	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12342166	1.00[EUR][1000 genomes]
rs12342282	1.00[EUR][1000 genomes]
rs12343325	1.00[EUR][1000 genomes]
rs12345849	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351533	1.00[EUR][1000 genomes]
rs12352918	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1411949	1.00[EUR][1000 genomes]
rs1993912	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28431078	1.00[EUR][1000 genomes]
rs28706504	1.00[EUR][1000 genomes]
rs386775	1.00[EUR][1000 genomes]
rs57154492	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58291302	1.00[EUR][1000 genomes]
rs60037728	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7022080	1.00[EUR][1000 genomes]
rs7029847	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383109	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383113	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383114	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73383144	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73385128	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73387085	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73397307	1.00[EUR][1000 genomes]
rs73397376	1.00[EUR][1000 genomes]
rs73399307	1.00[EUR][1000 genomes]
rs73639554	1.00[EUR][1000 genomes]
rs73639568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853706	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7858084	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv892155	chr9:5825768-6044937	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv892156	chr9:5892375-6011757	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1015450	chr9:5915640-6114652	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:5940000-6006800	Weak transcription	Gastric	stomach
2	chr9:5948000-6006000	Weak transcription	Right Ventricle	heart
3	chr9:5950600-6006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:5957400-6004400	Weak transcription	Brain Germinal Matrix	brain
5	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
6	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
7	chr9:5969400-5999600	Weak transcription	HSMMtube	muscle
8	chr9:5972200-6005800	Weak transcription	NH-A	brain
9	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:5974400-5999600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr9:5974800-6001000	Weak transcription	Fetal Brain Female	brain
12	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
13	chr9:5977400-6000800	Weak transcription	Small Intestine	intestine
14	chr9:5977400-6004800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:5977400-6005600	Weak transcription	NHLF	lung
16	chr9:5977400-6005800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
18	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
19	chr9:5982800-5999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr9:5982800-6005200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:5983200-5999400	Weak transcription	Brain Substantia Nigra	brain
22	chr9:5983200-6004200	Weak transcription	Osteobl	bone
23	chr9:5983400-6004200	Weak transcription	NHDF-Ad	bronchial
24	chr9:5984000-6001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:5987200-6000800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr9:5987200-6005200	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:5987200-6006200	Weak transcription	Thymus	Thymus
28	chr9:5987400-5999600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr9:5987400-6001200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:5987800-6004000	Weak transcription	Dnd41	blood
31	chr9:5987800-6004200	Weak transcription	Hela-S3	cervix
32	chr9:5988000-6003800	Weak transcription	Fetal Intestine Large	intestine
33	chr9:5988000-6004200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:5988000-6005600	Weak transcription	Adipose Nuclei	Adipose
35	chr9:5988000-6005600	Weak transcription	Fetal Lung	lung
36	chr9:5988000-6006200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:5988200-6003800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr9:5988200-6005600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:5988200-6005800	Weak transcription	HSMM	muscle
40	chr9:5988200-6006000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:5988600-5999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr9:5988600-5999600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr9:5988600-5999600	Weak transcription	GM12878-XiMat	blood
44	chr9:5988600-6004000	Weak transcription	Fetal Thymus	thymus
45	chr9:5988600-6004200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:5988600-6004600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr9:5988600-6004800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr9:5988600-6005800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr9:5988800-5999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:5988800-6000800	Weak transcription	Monocytes-CD14+_RO01746	blood

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