Variant report

Variant	rs6506540
Chromosome Location	chr18:7936938-7936939
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	chr18:7936902..7939574-chr18:7940048..7941947,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1016188	0.85[YRI][hapmap]
rs11081352	0.81[LWK][hapmap]
rs17566436	0.83[CHB][hapmap]
rs17566499	0.83[CHB][hapmap]
rs36008832	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786153	0.82[YRI][hapmap]
rs5003719	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6506542	0.81[LWK][hapmap];0.81[YRI][hapmap]
rs7228385	0.83[CHB][hapmap]
rs7238517	0.81[CHB][hapmap]
rs8082776	0.84[LWK][hapmap]
rs8087998	0.91[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8089387	0.81[LWK][hapmap]
rs8096083	0.83[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9956729	0.91[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9960576	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9964296	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv2761987	chr18:7934001-7943335	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7922400-7940600	Weak transcription	Gastric	stomach
2	chr18:7923400-7937400	Weak transcription	Right Ventricle	heart
3	chr18:7923400-7945800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr18:7923600-7937000	Weak transcription	Adipose Nuclei	Adipose
5	chr18:7924400-7940400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr18:7925800-7940400	Weak transcription	Fetal Muscle Leg	muscle
7	chr18:7926400-7940200	Weak transcription	Brain Germinal Matrix	brain
8	chr18:7926400-7945200	Weak transcription	Ovary	ovary
9	chr18:7926800-7945600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr18:7926800-7945800	Weak transcription	Fetal Lung	lung
11	chr18:7927400-7939800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr18:7927400-7940200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr18:7927800-7937400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr18:7927800-7946600	Weak transcription	Fetal Kidney	kidney
15	chr18:7928000-7946600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr18:7928200-7937400	Weak transcription	Left Ventricle	heart
17	chr18:7929600-7937000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr18:7932000-7946000	Weak transcription	Brain Anterior Caudate	brain
19	chr18:7932200-7961000	Weak transcription	HepG2	liver
20	chr18:7933400-7940400	Weak transcription	Lung	lung
21	chr18:7933600-7945400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr18:7933800-7940000	Weak transcription	Right Atrium	heart
23	chr18:7934200-7941000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:7935400-7937000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr18:7936200-7937600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr18:7936200-7937600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr18:7936200-7937600	Strong transcription	Thymus	Thymus
28	chr18:7936200-7937800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr18:7936400-7937000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:7936400-7937600	Enhancers	Spleen	Spleen
31	chr18:7936600-7937200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr18:7936600-7937400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
33	chr18:7936600-7937600	Strong transcription	Fetal Stomach	stomach
34	chr18:7936800-7937400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr18:7936800-7937600	Enhancers	Esophagus	oesophagus
36	chr18:7936800-7938000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr18:7936800-7938000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr18:7936800-7939800	Weak transcription	A549	lung
39	chr18:7936800-7940400	Weak transcription	Aorta	Aorta
40	chr18:7936800-7941000	Weak transcription	Pancreas	Pancrea
41	chr18:7936800-7944800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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