Variant report

Variant	rs683375
Chromosome Location	chr18:29840735-29840736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:29837235..29838765-chr18:29839489..29841604,2	MCF-7	breast:
2	chr18:29839871..29842778-chr18:29859077..29861521,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1614242	0.98[ASN][1000 genomes]
rs470958	0.98[ASN][1000 genomes]
rs606576	0.98[ASN][1000 genomes]
rs609285	1.00[CEU][hapmap]
rs613616	0.99[ASN][1000 genomes]
rs613941	1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs624130	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs624171	0.81[CEU][hapmap]
rs625863	1.00[ASN][1000 genomes]
rs635901	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs636809	1.00[ASN][1000 genomes]
rs638664	0.82[GIH][hapmap]
rs645526	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.98[ASN][1000 genomes]
rs646452	1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.95[ASN][1000 genomes]
rs647499	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs660959	0.83[EUR][1000 genomes]
rs669116	1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs676968	0.82[GIH][hapmap]
rs682459	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9510	0.81[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1056007	chr18:29711974-29899564	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv833616	chr18:29792336-29964212	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv528846	chr18:29832147-29890042	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs683375	KLHL14	cis	cerebellum	SCAN
rs683375	DSC2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29823800-29848000	Weak transcription	Aorta	Aorta
2	chr18:29831400-29847600	Weak transcription	Pancreas	Pancrea
3	chr18:29835200-29861600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr18:29837400-29847800	Weak transcription	Right Ventricle	heart
5	chr18:29837400-29867200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:29837600-29848200	Weak transcription	Colonic Mucosa	Colon
7	chr18:29838000-29847600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr18:29838000-29848000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr18:29838400-29847600	Weak transcription	Brain Hippocampus Middle	brain
10	chr18:29838600-29843200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr18:29838600-29848000	Weak transcription	HepG2	liver
12	chr18:29838600-29851400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr18:29838600-29851600	Weak transcription	Stomach Mucosa	stomach
14	chr18:29838800-29841800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr18:29838800-29846800	Weak transcription	Liver	Liver
16	chr18:29838800-29846800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr18:29839000-29847600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr18:29839000-29847800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr18:29839200-29843200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr18:29839200-29847600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr18:29839800-29844400	Weak transcription	Fetal Intestine Small	intestine
22	chr18:29839800-29871800	Weak transcription	HSMMtube	muscle
23	chr18:29840000-29847800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr18:29840200-29844200	Weak transcription	Fetal Intestine Large	intestine

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