Variant report

Variant	rs3777887
Chromosome Location	chr6:133836330-133836331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:133836320-133836470	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:133825151..133828230-chr6:133834384..133837130,3	MCF-7	breast:

Variant related genes	Relation type
HSPE1P21	TF binding region
ENSG00000227954	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11964505	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11964979	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11968532	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969376	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969485	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969724	0.89[CHB][hapmap]
rs11970169	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12110683	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053540	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17053541	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17053542	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17641157	1.00[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs17643040	1.00[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs3777867	1.00[CHB][hapmap]
rs3777876	1.00[CHB][hapmap]
rs3777881	0.90[CHB][hapmap]
rs3777886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3822937	0.89[CEU][hapmap];0.82[YRI][hapmap];0.90[EUR][1000 genomes]
rs3822938	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4053065	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41286206	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41286212	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865377	0.82[EUR][1000 genomes]
rs55903152	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59080198	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60337650	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60797218	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67351386	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67720873	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912858	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6921393	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929938	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6934616	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73003668	0.87[ASN][1000 genomes]
rs7453259	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7743115	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7749529	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7767007	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7771096	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7771144	0.83[EUR][1000 genomes];0.98[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	nsv886681	chr6:133833284-133869617	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3777887	SAMD3	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133823200-133869600	Weak transcription	Psoas Muscle	Psoas
2	chr6:133824200-133854200	Weak transcription	Fetal Muscle Leg	muscle
3	chr6:133824400-133837400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:133824400-133854800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:133824400-133861600	Weak transcription	Ovary	ovary
6	chr6:133825600-133857200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:133826400-133844800	Weak transcription	Fetal Kidney	kidney
8	chr6:133826600-133862400	Weak transcription	Fetal Lung	lung
9	chr6:133828800-133836800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:133832600-133836800	Strong transcription	Hela-S3	cervix
11	chr6:133835600-133837200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:133835800-133836800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr6:133836200-133837400	Strong transcription	A549	lung

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