Variant report

Variant	rs12607576
Chromosome Location	chr18:13246168-13246169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:13222557..13225016-chr18:13245739..13247328,2	MCF-7	breast:
2	chr18:13243981..13246911-chr18:13539689..13542169,2	MCF-7	breast:
3	chr18:13215937..13222150-chr18:13244092..13248320,7	MCF-7	breast:
4	chr18:13241697..13243575-chr18:13244259..13246294,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267239	Chromatin interaction
ENSG00000168675	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11662617	0.86[ASW][hapmap]
rs12455455	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12458598	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs12968748	0.93[CHD][hapmap];0.85[GIH][hapmap]
rs12969923	0.81[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs3901403	0.93[CHD][hapmap];0.85[GIH][hapmap];0.80[ASN][1000 genomes]
rs4277409	0.80[ASN][1000 genomes]
rs4797747	0.80[ASN][1000 genomes]
rs4797749	0.83[ASN][1000 genomes]
rs55962651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56191278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59835474	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62636871	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944928	0.91[CHD][hapmap];0.83[GIH][hapmap]
rs9952107	0.89[CHD][hapmap];0.81[GIH][hapmap]

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	nsv833591	chr18:13093777-13253748	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv909408	chr18:13122618-13308950	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv909410	chr18:13151544-13308950	Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12607576	TUBB6	cis	cerebellum	SCAN
rs12607576	C18orf19	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:13223800-13259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr18:13224000-13259800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr18:13224400-13259800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr18:13232800-13246200	Weak transcription	Psoas Muscle	Psoas
5	chr18:13233000-13260200	Weak transcription	Colonic Mucosa	Colon
6	chr18:13233400-13254000	Weak transcription	Spleen	Spleen
7	chr18:13233400-13259000	Weak transcription	Primary T cells from cord blood	blood
8	chr18:13236200-13258800	Weak transcription	Fetal Lung	lung
9	chr18:13237400-13258800	Weak transcription	Adipose Nuclei	Adipose
10	chr18:13237400-13258800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr18:13237800-13258800	Weak transcription	Colon Smooth Muscle	Colon
12	chr18:13239600-13255800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr18:13240200-13246200	Weak transcription	Liver	Liver
14	chr18:13240200-13256000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr18:13240400-13246400	Weak transcription	Fetal Muscle Leg	muscle
16	chr18:13240600-13246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr18:13240600-13252400	Weak transcription	Brain Hippocampus Middle	brain
18	chr18:13240600-13252600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr18:13243200-13260200	Weak transcription	Aorta	Aorta
20	chr18:13243600-13278200	Weak transcription	Dnd41	blood
21	chr18:13243800-13252800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr18:13243800-13252800	Weak transcription	Fetal Stomach	stomach
23	chr18:13244400-13246800	Enhancers	Fetal Brain Male	brain
24	chr18:13244800-13247200	Enhancers	Fetal Brain Female	brain
25	chr18:13245000-13246400	Enhancers	Gastric	stomach
26	chr18:13245200-13246800	Enhancers	Left Ventricle	heart
27	chr18:13245200-13247200	Enhancers	Fetal Heart	heart
28	chr18:13245400-13253000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr18:13245600-13246200	Genic enhancers	Fetal Thymus	thymus
30	chr18:13245600-13246400	Enhancers	Right Ventricle	heart
31	chr18:13245600-13247000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr18:13245800-13246400	Enhancers	Right Atrium	heart
33	chr18:13246000-13246600	Enhancers	Brain Anterior Caudate	brain
34	chr18:13246000-13246600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr18:13246000-13247600	Weak transcription	Brain Germinal Matrix	brain
36	chr18:13246000-13248600	Strong transcription	Thymus	Thymus

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