Variant report

Variant	rs35959277
Chromosome Location	chr18:12285181-12285182
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12281847..12285413-chr18:12286066..12289370,4	MCF-7	breast:
2	chr18:12284795..12287188-chr18:12289941..12291759,2	K562	blood:
3	chr18:12283750..12286656-chr18:12370266..12373091,2	K562	blood:
4	chr18:12282475..12288140-chr18:12305542..12311210,9	K562	blood:
5	chr18:12276259..12278951-chr18:12284988..12286490,2	K562	blood:
6	chr18:12284886..12287018-chr18:12289577..12291293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction
ENSG00000267069	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11661431	0.82[ASN][1000 genomes]
rs12455756	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12455885	0.81[ASN][1000 genomes]
rs12607250	0.84[ASN][1000 genomes]
rs12954560	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12960302	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12965912	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs28625182	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34685983	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61604633	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62097556	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7244709	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9303766	0.84[ASN][1000 genomes]
rs9303767	0.84[ASN][1000 genomes]
rs9303768	0.83[ASN][1000 genomes]
rs9807444	0.84[ASN][1000 genomes]
rs9945901	0.84[ASN][1000 genomes]
rs9946172	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9946217	0.84[ASN][1000 genomes]
rs9946347	0.84[ASN][1000 genomes]
rs9949054	0.84[ASN][1000 genomes]
rs9954945	0.84[ASN][1000 genomes]
rs9958069	0.84[ASN][1000 genomes]
rs9958525	0.84[ASN][1000 genomes]
rs9964163	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
8	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
10	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv870342	chr18:12270808-12295798	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs35959277	TUBB6	cis	multi-tissue	Pritchard
rs35959277	TUBB6	cis	Whole Blood	GTEx
rs35959277	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs35959277	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12279600-12287600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr18:12280000-12287400	Weak transcription	Right Atrium	heart
3	chr18:12280000-12287800	Weak transcription	Ovary	ovary
4	chr18:12280400-12287400	Weak transcription	Adipose Nuclei	Adipose
5	chr18:12280400-12287600	Weak transcription	Aorta	Aorta
6	chr18:12280400-12287600	Weak transcription	Lung	lung
7	chr18:12281800-12287000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr18:12281800-12287400	Weak transcription	Left Ventricle	heart
9	chr18:12283000-12286800	Weak transcription	Fetal Muscle Leg	muscle
10	chr18:12283000-12287000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr18:12283000-12287200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr18:12283000-12287200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr18:12283000-12287200	Weak transcription	Right Ventricle	heart
14	chr18:12283000-12287200	Weak transcription	Hela-S3	cervix
15	chr18:12283200-12286000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr18:12283200-12287200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr18:12283200-12287200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr18:12283200-12287400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr18:12283200-12287400	Weak transcription	Osteobl	bone
20	chr18:12283200-12287800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr18:12283400-12287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr18:12283400-12287000	Weak transcription	HMEC	breast
23	chr18:12283400-12287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:12283400-12287200	Weak transcription	NH-A	brain
25	chr18:12283600-12287000	Weak transcription	HSMM	muscle
26	chr18:12283600-12287200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr18:12283600-12287400	Weak transcription	NHDF-Ad	bronchial
28	chr18:12284000-12287000	Weak transcription	NHEK	skin
29	chr18:12284000-12287200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:12284000-12287400	Weak transcription	HUVEC	blood vessel
31	chr18:12284000-12287400	Weak transcription	NHLF	lung
32	chr18:12284200-12287200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr18:12284400-12285200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr18:12284400-12287200	Weak transcription	Fetal Heart	heart
35	chr18:12284600-12287200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr18:12284800-12285200	Enhancers	HSMMtube	muscle
37	chr18:12284800-12287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr18:12284800-12287200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr18:12284800-12287800	Weak transcription	K562	blood

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