Variant report

Variant	rs787554
Chromosome Location	chr18:11862697-11862698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:11853567..11855306-chr18:11862502..11865117,2	K562	blood:
2	chr18:11855790..11858853-chr18:11861688..11864675,4	K562	blood:
3	chr18:11851574..11853524-chr18:11861747..11863515,2	MCF-7	breast:
4	chr18:11850500..11852833-chr18:11861149..11862770,2	K562	blood:
5	chr18:11856529..11858770-chr18:11861924..11864675,2	K562	blood:
6	chr18:11856045..11858949-chr18:11860303..11863306,3	MCF-7	breast:
7	chr18:11849782..11853357-chr18:11861149..11865205,5	K562	blood:

Variant related genes	Relation type
ENSG00000141404	Chromatin interaction
ENSG00000267165	Chromatin interaction
ENSG00000255112	Chromatin interaction
ENSG00000272703	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11874959	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12454601	0.91[ASN][1000 genomes]
rs16976774	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071138	1.00[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2071139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2071140	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2071141	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2586208	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2586211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2586214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2848454	1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2848455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2848462	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848463	1.00[CEU][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2848464	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2848466	0.91[ASN][1000 genomes]
rs2848467	0.91[ASN][1000 genomes]
rs2855638	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2855639	1.00[CEU][hapmap]
rs2855645	0.81[EUR][1000 genomes]
rs2855646	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2855648	0.91[ASN][1000 genomes]
rs2855649	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2859542	1.00[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs72870404	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs787557	0.96[ASN][1000 genomes]
rs787558	0.95[ASN][1000 genomes]
rs787559	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9303750	0.96[ASN][1000 genomes]
rs9303751	0.96[ASN][1000 genomes]
rs9947329	0.91[ASN][1000 genomes]
rs9947607	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3362008	chr18:11647654-11959830	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv833590	chr18:11757329-11924539	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv1055453	chr18:11776790-12110135	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv543654	chr18:11776790-12110135	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs787554	GNAL	cis	parietal	SCAN
rs787554	FLJ37201	trans	cerebellum	SCAN
rs787554	TWSG1	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:11852400-11880800	Weak transcription	Aorta	Aorta
2	chr18:11853600-11883800	Weak transcription	Ovary	ovary
3	chr18:11853800-11884200	Weak transcription	Brain Substantia Nigra	brain
4	chr18:11854000-11875000	Weak transcription	Brain Hippocampus Middle	brain
5	chr18:11854000-11884200	Weak transcription	Brain Angular Gyrus	brain
6	chr18:11854200-11868200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr18:11854400-11868400	Weak transcription	Primary B cells from cord blood	blood
8	chr18:11854800-11889200	Weak transcription	Fetal Brain Male	brain
9	chr18:11855400-11875400	Weak transcription	Fetal Stomach	stomach
10	chr18:11855600-11880800	Weak transcription	Fetal Brain Female	brain
11	chr18:11856600-11865000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr18:11857600-11872800	Weak transcription	Left Ventricle	heart
13	chr18:11857800-11862800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr18:11857800-11866000	Weak transcription	Brain Anterior Caudate	brain
15	chr18:11857800-11867000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr18:11857800-11868400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr18:11857800-11875200	Weak transcription	Brain Germinal Matrix	brain
18	chr18:11857800-11876400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr18:11858000-11865000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr18:11858000-11868400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr18:11858000-11868400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr18:11858200-11884000	Weak transcription	Colon Smooth Muscle	Colon
23	chr18:11858600-11868400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr18:11858600-11875800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:11858600-11879400	Weak transcription	Adipose Nuclei	Adipose
26	chr18:11859000-11886400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr18:11859200-11875600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr18:11859600-11866600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr18:11860200-11875200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr18:11860200-11875400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:11860800-11862800	Enhancers	HepG2	liver
32	chr18:11860800-11863200	Weak transcription	Fetal Intestine Large	intestine
33	chr18:11860800-11864600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr18:11860800-11865400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr18:11860800-11868400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:11861000-11864400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr18:11861000-11880800	Weak transcription	Esophagus	oesophagus
38	chr18:11861600-11873400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr18:11861800-11872600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr18:11861800-11887800	Weak transcription	Psoas Muscle	Psoas
41	chr18:11862000-11863400	Enhancers	Fetal Intestine Small	intestine
42	chr18:11862000-11865200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr18:11862200-11862800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr18:11862200-11862800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr18:11862200-11862800	Enhancers	Stomach Mucosa	stomach
46	chr18:11862400-11863000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr18:11862400-11863400	Weak transcription	A549	lung
48	chr18:11862400-11871400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr18:11862400-11879200	Weak transcription	Spleen	Spleen
50	chr18:11862600-11862800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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