Variant report

Variant	rs4384658
Chromosome Location	chr18:9653171-9653172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9653164..9654681-chr18:9657331..9659688,2	MCF-7	breast:
2	chr18:9612188..9615434-chr18:9650562..9653752,4	MCF-7	breast:
3	chr18:9643875..9645659-chr18:9651829..9653489,2	MCF-7	breast:
4	chr18:9647445..9649188-chr18:9652519..9654755,2	K562	blood:
5	chr18:9613284..9616245-chr18:9652584..9654808,2	MCF-7	breast:
6	chr18:9643047..9645539-chr18:9651968..9654272,3	MCF-7	breast:
7	chr18:9643919..9647276-chr18:9653045..9655313,3	K562	blood:
8	chr18:9629058..9631077-chr18:9650339..9653253,2	K562	blood:

Variant related genes	Relation type
ENSG00000154845	Chromatin interaction
ENSG00000263627	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12957571	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12959303	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12960645	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955402	0.85[JPT][hapmap]
rs2061136	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2061139	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55818445	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609427	0.82[JPT][hapmap]
rs62080347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663000	0.82[JPT][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	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4384658	SEH1L	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9639200-9663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:9648200-9653200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr18:9648200-9653200	Weak transcription	HUVEC	blood vessel
4	chr18:9648200-9653400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:9648600-9654800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr18:9649600-9653400	Weak transcription	HMEC	breast
7	chr18:9649600-9658600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr18:9649800-9661200	Weak transcription	A549	lung
9	chr18:9650000-9653200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr18:9650000-9653400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr18:9650000-9653400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:9650000-9654800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr18:9650000-9657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:9650000-9657200	Weak transcription	NHEK	skin
15	chr18:9650400-9654800	Weak transcription	NHDF-Ad	bronchial
16	chr18:9652200-9653200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr18:9652200-9653800	Enhancers	Esophagus	oesophagus
18	chr18:9652600-9653200	Enhancers	Placenta	Placenta
19	chr18:9652800-9653400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr18:9652800-9653600	Enhancers	Brain Substantia Nigra	brain
21	chr18:9652800-9653600	Enhancers	Pancreas	Pancrea
22	chr18:9652800-9654000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr18:9652800-9655000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:9652800-9655000	Enhancers	Brain Cingulate Gyrus	brain
25	chr18:9653000-9653200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:9653000-9653400	Enhancers	Brain Anterior Caudate	brain
27	chr18:9653000-9653600	Enhancers	Aorta	Aorta
28	chr18:9653000-9653600	Enhancers	Brain Angular Gyrus	brain
29	chr18:9653000-9653600	Enhancers	Brain Hippocampus Middle	brain
30	chr18:9653000-9653800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr18:9653000-9654200	Enhancers	Hela-S3	cervix
32	chr18:9653000-9654800	Enhancers	HepG2	liver

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