Variant report

Variant	rs9387177
Chromosome Location	chr6:114082458-114082459
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	chr6:114080493..114083851-chr6:114178361..114180752,3	MCF-7	breast:
2	chr6:114078677..114080335-chr6:114081487..114084433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155130	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13209042	0.85[CHB][hapmap];0.91[CHD][hapmap]
rs17075611	0.86[AMR][1000 genomes]
rs2018090	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2463310	0.83[ASN][1000 genomes]
rs2615518	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2695451	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2695452	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2810179	0.85[CHB][hapmap];0.93[CHD][hapmap]
rs2810182	0.83[AMR][1000 genomes]
rs2810188	0.83[AMR][1000 genomes]
rs2810189	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2810191	0.83[AMR][1000 genomes]
rs2810195	0.85[CHB][hapmap]
rs34777588	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4496829	0.88[ASN][1000 genomes]
rs4574672	1.00[ASN][1000 genomes]
rs55705700	0.94[ASN][1000 genomes]
rs6568807	1.00[ASN][1000 genomes]
rs6918103	0.99[ASN][1000 genomes]
rs6923574	0.98[ASN][1000 genomes]
rs6940434	0.99[ASN][1000 genomes]
rs71553754	0.91[ASN][1000 genomes]
rs773685	0.95[JPT][hapmap]
rs7760821	0.99[ASN][1000 genomes]
rs7765004	0.98[ASN][1000 genomes]
rs9372374	0.98[ASN][1000 genomes]
rs9372376	0.97[ASN][1000 genomes]
rs9374426	0.98[ASN][1000 genomes]
rs9374427	0.91[ASN][1000 genomes]
rs9384882	0.99[ASN][1000 genomes]
rs9387174	0.98[ASN][1000 genomes]
rs9387176	0.98[ASN][1000 genomes]
rs9400667	0.98[ASN][1000 genomes]
rs9400671	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9400672	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9400676	0.85[CHB][hapmap];0.91[CHD][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs949599	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs959211	0.85[CHB][hapmap]
rs963884	0.85[CHB][hapmap];0.93[CHD][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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv464023	chr6:114071720-114114057	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	nsv604532	chr6:114071720-114114057	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9387177	RWDD1	cis	cerebellum	SCAN
rs9387177	REV3L	cis	parietal	SCAN
rs9387177	KDM4D	trans	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114077000-114085000	Weak transcription	Psoas Muscle	Psoas
2	chr6:114077600-114083800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:114077600-114084600	Weak transcription	HSMM	muscle
4	chr6:114080400-114084200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:114080400-114085000	Weak transcription	A549	lung
6	chr6:114080600-114083400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:114080600-114083600	Weak transcription	HUVEC	blood vessel
8	chr6:114080600-114083800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:114080600-114083800	Weak transcription	Fetal Lung	lung
10	chr6:114080600-114083800	Weak transcription	Osteobl	bone
11	chr6:114080600-114084000	Weak transcription	Placenta	Placenta
12	chr6:114080800-114083000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr6:114080800-114083400	Weak transcription	GM12878-XiMat	blood
14	chr6:114080800-114083400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:114080800-114083800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr6:114080800-114083800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:114081400-114082800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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