Variant report

Variant	rs3904554
Chromosome Location	chr1:95246366-95246367
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	chr1:95239553..95241995-chr1:95245033..95246772,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10782992	1.00[ASN][1000 genomes]
rs10782993	1.00[ASN][1000 genomes]
rs10874894	0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs1146458	1.00[ASN][1000 genomes]
rs2893277	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3860339	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3860345	1.00[ASN][1000 genomes]
rs3860348	1.00[ASN][1000 genomes]
rs3860349	0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs3904553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3916208	1.00[ASN][1000 genomes]
rs3916432	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4847359	1.00[GIH][hapmap];0.88[YRI][hapmap];1.00[ASN][1000 genomes]
rs6541370	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6541372	1.00[ASN][1000 genomes]
rs6665321	1.00[ASN][1000 genomes]
rs6702030	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7528707	1.00[ASN][1000 genomes]
rs7543977	1.00[ASN][1000 genomes]
rs9432373	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95239200-95248600	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:95239400-95249000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:95240000-95247000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:95240000-95249000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:95240800-95249000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:95242400-95248600	Weak transcription	HMEC	breast
7	chr1:95242600-95248800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:95242600-95249000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:95242600-95249000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:95242600-95249000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:95242600-95268000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:95243000-95249000	Weak transcription	Fetal Intestine Small	intestine
13	chr1:95243200-95246800	Weak transcription	Pancreas	Pancrea
14	chr1:95243200-95265000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:95243400-95248800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:95244600-95247800	Weak transcription	Stomach Mucosa	stomach
17	chr1:95244800-95251000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:95245000-95247800	Weak transcription	Hela-S3	cervix
19	chr1:95245000-95248200	Weak transcription	NHDF-Ad	bronchial
20	chr1:95245200-95248200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:95245600-95249000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:95245800-95248600	Weak transcription	NHLF	lung
23	chr1:95245800-95248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:95245800-95248800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:95245800-95249000	Weak transcription	Lung	lung
26	chr1:95246200-95248600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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