Variant report

Variant	rs4796961
Chromosome Location	chr18:12320191-12320192
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	chr18:12307701..12309556-chr18:12318033..12320333,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10459999	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10460000	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10460001	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10853225	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11080564	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080565	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080569	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11080571	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11080572	0.85[AMR][1000 genomes]
rs1129115	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11662523	0.85[AMR][1000 genomes]
rs11664216	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11665134	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455273	0.83[AMR][1000 genomes]
rs12456857	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12604732	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12954686	0.89[AMR][1000 genomes]
rs12968566	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34829762	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35338639	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4796964	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4797677	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62098961	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7231409	0.85[AMR][1000 genomes]
rs7235237	0.85[AMR][1000 genomes]
rs7235296	0.85[AMR][1000 genomes]
rs7407640	0.80[AMR][1000 genomes]
rs7504908	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7504974	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7505834	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8086821	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8086993	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8087840	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8092506	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8097342	0.80[AMR][1000 genomes]
rs9303769	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9946698	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9951945	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4796961	TUBB6	cis	Whole Blood	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12310000-12324800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:12310000-12325800	Weak transcription	Fetal Kidney	kidney
3	chr18:12310200-12320400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr18:12310200-12324800	Weak transcription	HepG2	liver
5	chr18:12310600-12322800	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr18:12311000-12323200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:12311000-12324800	Weak transcription	Spleen	Spleen
8	chr18:12312600-12320400	Weak transcription	Brain Angular Gyrus	brain
9	chr18:12312600-12325000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr18:12312600-12332600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12312800-12324800	Weak transcription	Colonic Mucosa	Colon
12	chr18:12312800-12324800	Weak transcription	Fetal Brain Female	brain
13	chr18:12313000-12320800	Weak transcription	Fetal Intestine Small	intestine
14	chr18:12313200-12320400	Weak transcription	Liver	Liver
15	chr18:12314000-12333600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr18:12314200-12323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr18:12314200-12327800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr18:12314400-12342600	Weak transcription	Small Intestine	intestine
19	chr18:12314600-12324400	Weak transcription	Brain Germinal Matrix	brain
20	chr18:12314800-12320600	Weak transcription	Fetal Intestine Large	intestine
21	chr18:12315600-12324800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr18:12316200-12320600	Weak transcription	Brain Substantia Nigra	brain
23	chr18:12316200-12324600	Weak transcription	Gastric	stomach
24	chr18:12316200-12325000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:12316400-12320600	Weak transcription	Brain Anterior Caudate	brain
26	chr18:12316400-12323000	Weak transcription	Fetal Lung	lung
27	chr18:12316400-12333600	Weak transcription	Fetal Brain Male	brain
28	chr18:12316600-12324400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:12316600-12324800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr18:12316600-12327000	Weak transcription	Stomach Mucosa	stomach
31	chr18:12316800-12320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr18:12316800-12320600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr18:12316800-12321600	Strong transcription	NHEK	skin
34	chr18:12316800-12327600	Strong transcription	HUVEC	blood vessel
35	chr18:12317600-12324800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr18:12317800-12322200	Strong transcription	NH-A	brain
37	chr18:12318000-12321000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr18:12318000-12321200	Strong transcription	HSMM	muscle
39	chr18:12318000-12325000	Weak transcription	Hela-S3	cervix
40	chr18:12318000-12331200	Strong transcription	HMEC	breast
41	chr18:12318200-12320400	Strong transcription	Osteobl	bone
42	chr18:12318400-12320400	Strong transcription	HSMMtube	muscle
43	chr18:12318400-12320600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:12318400-12320800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr18:12318400-12321200	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr18:12318400-12321400	Weak transcription	Pancreas	Pancrea
47	chr18:12318400-12324800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr18:12318400-12334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:12318600-12320400	Weak transcription	K562	blood
50	chr18:12318600-12320600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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