Variant report

Variant	rs6603030
Chromosome Location	chr15:83230103-83230104
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:83226594..83230690-chr15:83232358..83235260,6	K562	blood:
2	chr15:83217765..83219665-chr15:83228669..83230495,2	K562	blood:
3	chr15:83229777..83231683-chr15:83417698..83419627,2	K562	blood:
4	chr15:83229558..83232531-chr15:83236614..83238235,2	K562	blood:

Variant related genes	Relation type
ENSG00000250988	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11631033	0.82[MEX][hapmap]
rs11631182	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs11633991	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap]
rs11635044	0.92[CHB][hapmap]
rs11635357	0.82[MEX][hapmap]
rs11635442	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs11635460	0.92[CHB][hapmap];0.93[CHD][hapmap]
rs11635476	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs11635624	0.91[GIH][hapmap]
rs11638815	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1267656	0.95[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1431717	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.82[AMR][1000 genomes]
rs1877242	0.92[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap]
rs2379997	0.82[CHB][hapmap]
rs4779041	0.91[GIH][hapmap]
rs4779048	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4779049	0.85[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7171180	0.91[GIH][hapmap]
rs7182320	0.92[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap]
rs783542	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs783544	0.84[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8033106	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]

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	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6603030	FAM154B	cis	parietal	SCAN
rs6603030	RP13-608F4.1	cis	Esophagus Mucosa	GTEx
rs6603030	RASGRF1	cis	cerebellum	SCAN
rs6603030	GOLGA6L10	cis	Esophagus Mucosa	GTEx
rs6603030	AP3B2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83216800-83235000	Weak transcription	NHLF	lung
2	chr15:83219000-83239400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:83219800-83239800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:83222000-83235200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr15:83222000-83239200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:83222200-83237800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:83222600-83239400	Weak transcription	Fetal Stomach	stomach
8	chr15:83222600-83239600	Weak transcription	Ovary	ovary
9	chr15:83222600-83239600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:83222800-83240600	Weak transcription	Aorta	Aorta
11	chr15:83223400-83230200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:83223800-83233800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:83223800-83239600	Weak transcription	Brain Substantia Nigra	brain
14	chr15:83224800-83232600	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:83224800-83233400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:83224800-83233800	Weak transcription	Brain Anterior Caudate	brain
17	chr15:83224800-83235400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:83224800-83239800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr15:83226000-83233400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr15:83226600-83232200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:83227000-83233400	Weak transcription	Brain Angular Gyrus	brain
22	chr15:83227600-83232400	Weak transcription	K562	blood
23	chr15:83227800-83231200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:83229400-83230600	Enhancers	Brain Inferior Temporal Lobe	brain

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