Variant report

Variant	rs12352918
Chromosome Location	chr9:5992351-5992352
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10116214	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10124484	1.00[CHB][hapmap]
rs10125832	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10975367	0.84[AFR][1000 genomes]
rs10975372	0.92[AFR][1000 genomes]
rs10975377	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs11793956	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12337790	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs12339713	0.88[AFR][1000 genomes]
rs12339886	0.95[YRI][hapmap];0.90[AFR][1000 genomes]
rs12339889	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12340531	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12341021	1.00[CHB][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12342282	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs12345849	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1330124	1.00[CHB][hapmap]
rs1993912	1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380568	1.00[CHB][hapmap]
rs58291302	0.88[AFR][1000 genomes]
rs73383109	0.87[AFR][1000 genomes]
rs73383113	0.90[AFR][1000 genomes]
rs73383114	0.90[AFR][1000 genomes]
rs73385128	0.88[AFR][1000 genomes]
rs73387085	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389036	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73389044	0.83[AMR][1000 genomes]
rs73639568	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7853706	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854980	0.90[AFR][1000 genomes]
rs7858084	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7858846	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7859471	1.00[CHB][hapmap]
rs7875607	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9299025	0.93[AFR][1000 genomes];0.83[AMR][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:104 , 50 per page) page: 1 2 3

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	chr9:5955000-5993600	Weak transcription	Lung	lung
5	chr9:5957400-6004400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:5967000-5996600	Weak transcription	Brain Angular Gyrus	brain
7	chr9:5967200-6006000	Weak transcription	Colonic Mucosa	Colon
8	chr9:5968400-6005600	Weak transcription	Fetal Kidney	kidney
9	chr9:5969200-5996800	Weak transcription	HMEC	breast
10	chr9:5969400-5999600	Weak transcription	HSMMtube	muscle
11	chr9:5972200-6005800	Weak transcription	NH-A	brain
12	chr9:5974000-6006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:5974400-5999600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:5974800-6001000	Weak transcription	Fetal Brain Female	brain
15	chr9:5975200-6005800	Weak transcription	Fetal Stomach	stomach
16	chr9:5977200-5997000	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:5977400-5993400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr9:5977400-5994400	Weak transcription	K562	blood
19	chr9:5977400-5996200	Weak transcription	Psoas Muscle	Psoas
20	chr9:5977400-5996600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:5977400-5996800	Weak transcription	Stomach Mucosa	stomach
22	chr9:5977400-6000800	Weak transcription	Small Intestine	intestine
23	chr9:5977400-6004800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:5977400-6005600	Weak transcription	NHLF	lung
25	chr9:5977400-6005800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr9:5977400-6006800	Weak transcription	Pancreas	Pancrea
27	chr9:5977400-6007000	Weak transcription	Spleen	Spleen
28	chr9:5978800-5994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:5982600-5995600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:5982800-5993600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr9:5982800-5999400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:5982800-6005200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr9:5983200-5993600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr9:5983200-5993600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr9:5983200-5996800	Weak transcription	NHEK	skin
36	chr9:5983200-5999400	Weak transcription	Brain Substantia Nigra	brain
37	chr9:5983200-6004200	Weak transcription	Osteobl	bone
38	chr9:5983400-5996600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:5983400-6004200	Weak transcription	NHDF-Ad	bronchial
40	chr9:5984000-6001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr9:5986600-5996400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr9:5987200-5993600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:5987200-6000800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr9:5987200-6005200	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:5987200-6006200	Weak transcription	Thymus	Thymus
46	chr9:5987400-5992800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:5987400-5994000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:5987400-5999600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:5987400-6001200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:5987600-5996800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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