Variant report

Variant	rs9946468
Chromosome Location	chr18:9202468-9202469
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9199977..9204433-chr18:9205247..9208292,4	K562	blood:
2	chr18:9201149..9204433-chr18:9205696..9208292,3	K562	blood:
3	chr18:9202054..9204266-chr18:9211528..9213526,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10451358	0.86[CHB][hapmap]
rs11661711	0.96[CEU][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap]
rs12150725	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12958093	0.95[CEU][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1443596	0.86[CHB][hapmap]
rs17413793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1893198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2028656	0.87[CHB][hapmap]
rs2155707	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28418978	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34310409	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34452937	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4078337	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs4131992	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4148967	0.96[CEU][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4603624	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs4797356	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs4797361	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4798772	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4798776	0.90[CEU][hapmap];0.85[CHB][hapmap];0.96[YRI][hapmap]
rs4798778	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs4798782	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4798784	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4798785	0.86[CHB][hapmap]
rs4798786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4798788	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4798789	0.87[CHB][hapmap]
rs4798790	0.87[CHB][hapmap]
rs4798791	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56317320	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6506644	0.82[CHB][hapmap]
rs6506648	0.86[CHB][hapmap]
rs6506649	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7228251	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7229883	0.81[CHB][hapmap]
rs7231452	0.86[CHB][hapmap]
rs7232337	0.96[ASN][1000 genomes]
rs7235514	0.82[CHB][hapmap]
rs7504603	0.90[CEU][hapmap];0.96[YRI][hapmap]
rs7506008	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7506291	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs8087306	0.91[JPT][hapmap]
rs8089693	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8092135	0.86[CHB][hapmap]
rs8097848	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs874250	0.86[CHB][hapmap]
rs894755	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9304033	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304034	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9304036	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs977581	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs9944905	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9945360	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9946475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946695	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs9946852	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9947027	0.96[CEU][hapmap];0.87[JPT][hapmap]
rs9948560	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9959998	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9960129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs998171	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1055696	chr18:9191679-9309805	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9946468	TWSG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9172000-9216200	Weak transcription	Fetal Brain Female	brain
2	chr18:9173000-9208400	Weak transcription	NHLF	lung
3	chr18:9174600-9233600	Weak transcription	Spleen	Spleen
4	chr18:9174800-9211000	Weak transcription	Hela-S3	cervix
5	chr18:9174800-9233600	Weak transcription	Pancreas	Pancrea
6	chr18:9178000-9221800	Weak transcription	Fetal Heart	heart
7	chr18:9180200-9214200	Weak transcription	A549	lung
8	chr18:9181600-9214200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr18:9183400-9211400	Weak transcription	Brain Germinal Matrix	brain
10	chr18:9183800-9225600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr18:9184600-9233800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr18:9185200-9233800	Weak transcription	Right Ventricle	heart
13	chr18:9185400-9214200	Weak transcription	Rectal Smooth Muscle	rectum
14	chr18:9185400-9223400	Weak transcription	Stomach Mucosa	stomach
15	chr18:9185600-9211000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr18:9185600-9232400	Weak transcription	Colonic Mucosa	Colon
17	chr18:9185800-9215200	Weak transcription	Small Intestine	intestine
18	chr18:9186000-9203800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:9186000-9214400	Weak transcription	Brain Angular Gyrus	brain
20	chr18:9187000-9221800	Weak transcription	Fetal Brain Male	brain
21	chr18:9188400-9214400	Weak transcription	Brain Anterior Caudate	brain
22	chr18:9188400-9233600	Weak transcription	Esophagus	oesophagus
23	chr18:9188600-9204000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr18:9188600-9205400	Weak transcription	Colon Smooth Muscle	Colon
25	chr18:9188600-9233600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr18:9188800-9211600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr18:9188800-9218200	Weak transcription	Thymus	Thymus
28	chr18:9189000-9203800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr18:9189000-9208400	Weak transcription	HSMMtube	muscle
30	chr18:9189200-9208600	Weak transcription	Ovary	ovary
31	chr18:9189200-9233800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr18:9189400-9203800	Weak transcription	Fetal Thymus	thymus
33	chr18:9189400-9215000	Weak transcription	Aorta	Aorta
34	chr18:9192200-9210400	Weak transcription	Left Ventricle	heart
35	chr18:9192200-9215400	Weak transcription	Psoas Muscle	Psoas
36	chr18:9192200-9233600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr18:9192200-9284000	Weak transcription	NHEK	skin
38	chr18:9192400-9211600	Weak transcription	HMEC	breast
39	chr18:9192400-9214400	Weak transcription	Fetal Muscle Leg	muscle
40	chr18:9192800-9203600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr18:9192800-9204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr18:9193000-9211400	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr18:9193200-9211200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr18:9193400-9224800	Weak transcription	Lung	lung
45	chr18:9193400-9230600	Weak transcription	Fetal Stomach	stomach
46	chr18:9193800-9211600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr18:9194200-9206000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr18:9194200-9211400	Weak transcription	NH-A	brain
49	chr18:9194800-9219400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr18:9195200-9203800	Weak transcription	Duodenum Mucosa	Duodenum

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