Variant report

Variant	rs633907
Chromosome Location	chr18:9642637-9642638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9637061..9640955-chr18:9641542..9645147,4	MCF-7	breast:
2	chr18:9613070..9618286-chr18:9641748..9647088,7	MCF-7	breast:
3	chr18:9612039..9617302-chr18:9635697..9643000,12	MCF-7	breast:
4	chr18:9633615..9636124-chr18:9641981..9643661,2	K562	blood:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000263627	Chromatin interaction
ENSG00000212572	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1787166	0.85[CHB][hapmap]
rs2289684	0.85[CHB][hapmap]
rs328995	0.82[CHB][hapmap]
rs329008	0.85[CHB][hapmap]
rs329024	0.85[CHB][hapmap]
rs329033	0.82[CHB][hapmap]
rs407530	0.85[CHB][hapmap]
rs428598	0.85[CHB][hapmap]
rs589559	0.85[CHB][hapmap]
rs645914	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689223	0.89[CEU][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs694861	0.85[CHB][hapmap]
rs7238204	0.88[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	esv3693417	chr18:9512985-9693638	Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv458024	chr18:9558240-9828448	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv576448	chr18:9558240-9828448	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
4	nsv576449	chr18:9623052-9700382	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs633907	VAPA	cis	parietal	SCAN
rs633907	PPP4R1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9628000-9642800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr18:9632400-9647600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr18:9639000-9648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:9639200-9642800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:9639200-9643000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr18:9639200-9663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr18:9639400-9642800	Weak transcription	Osteobl	bone
8	chr18:9639400-9643000	Weak transcription	A549	lung
9	chr18:9639600-9643000	Weak transcription	HUVEC	blood vessel
10	chr18:9640600-9643400	Enhancers	Placenta	Placenta
11	chr18:9641000-9642800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:9641000-9643000	Enhancers	NHEK	skin
13	chr18:9641000-9643600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:9641600-9645000	Enhancers	HMEC	breast
15	chr18:9641600-9645200	Enhancers	NHDF-Ad	bronchial
16	chr18:9641600-9645200	Enhancers	NHLF	lung
17	chr18:9641800-9642800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr18:9641800-9643000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr18:9641800-9645200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr18:9642000-9643400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr18:9642000-9643800	Enhancers	Fetal Muscle Leg	muscle
22	chr18:9642000-9644200	Enhancers	H1 Cell Line	embryonic stem cell
23	chr18:9642200-9643400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:9642200-9644400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr18:9642200-9644600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr18:9642400-9643800	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr18:9642400-9644000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr18:9642400-9644200	Enhancers	Colon Smooth Muscle	Colon
29	chr18:9642600-9643000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr18:9642600-9643200	Enhancers	Muscle Satellite Cultured Cells	--
31	chr18:9642600-9643800	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr18:9642600-9643800	Enhancers	NH-A	brain
33	chr18:9642600-9644600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr18:9642600-9647600	Weak transcription	H9 Cell Line	embryonic stem cell

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