Variant report

Variant	rs1023330
Chromosome Location	chr1:95586773-95586774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:95580754..95585035-chr1:95586074..95591340,6	K562	blood:
2	chr1:95391699..95393839-chr1:95586395..95588309,2	K562	blood:
3	chr1:95586523..95590030-chr1:95590782..95594117,4	K562	blood:

Variant related genes	Relation type
ENSG00000152078	Chromatin interaction
ENSG00000206679	Chromatin interaction
ENSG00000235501	Chromatin interaction
ENSG00000271092	Chromatin interaction
ENSG00000117519	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10735790	0.82[CHB][hapmap]
rs10874902	0.84[CHB][hapmap]
rs11585462	0.83[CHB][hapmap]
rs12563424	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12563592	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12741128	0.84[CHB][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12748237	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2391388	0.82[JPT][hapmap]
rs2766010	0.95[CHD][hapmap]
rs4245670	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4339907	0.83[CHB][hapmap]
rs4344373	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4630159	0.84[CHB][hapmap];0.82[LWK][hapmap]
rs4949965	0.84[CHB][hapmap]
rs4950058	0.84[CHB][hapmap];0.82[LWK][hapmap]
rs4950077	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4950083	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675668	0.84[CHB][hapmap]
rs6687388	0.84[CHB][hapmap]
rs6698046	0.89[CHD][hapmap]
rs9437689	0.82[CHB][hapmap];0.81[JPT][hapmap]

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	nsv830636	chr1:95495849-95703126	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv870669	chr1:95586773-95690269	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1023330	F3	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95583800-95587600	Weak transcription	Gastric	stomach
2	chr1:95584000-95586800	Enhancers	Brain Substantia Nigra	brain
3	chr1:95584000-95587600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:95584000-95592600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:95584000-95629400	Weak transcription	Aorta	Aorta
6	chr1:95584200-95586800	Enhancers	Fetal Lung	lung
7	chr1:95584400-95587400	Weak transcription	Fetal Intestine Large	intestine
8	chr1:95584400-95587600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:95584400-95588400	Weak transcription	Hela-S3	cervix
10	chr1:95584400-95590400	Enhancers	HepG2	liver
11	chr1:95584400-95603400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr1:95584600-95588400	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:95584600-95602200	Weak transcription	Right Ventricle	heart
14	chr1:95585000-95589400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:95585200-95587000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr1:95585200-95587200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:95585200-95592200	Weak transcription	Psoas Muscle	Psoas
18	chr1:95585400-95636800	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:95585800-95586800	Weak transcription	Pancreas	Pancrea
20	chr1:95585800-95587000	Flanking Active TSS	Liver	Liver
21	chr1:95585800-95587000	Enhancers	Left Ventricle	heart
22	chr1:95585800-95588200	Genic enhancers	K562	blood
23	chr1:95586200-95586800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:95586200-95587400	Weak transcription	Fetal Heart	heart
25	chr1:95586400-95587600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:95586400-95587600	Weak transcription	A549	lung
27	chr1:95586400-95588000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr1:95586600-95586800	Enhancers	Brain Germinal Matrix	brain

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