Variant report

Variant	rs16954989
Chromosome Location	chr18:9353809-9353810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9351286..9353025-chr18:9353787..9355705,3	K562	blood:
2	chr18:9353039..9355036-chr18:9357647..9360441,2	MCF-7	breast:
3	chr18:9333696..9336862-chr18:9352134..9356614,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264964	Chromatin interaction
ENSG00000128791	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11081472	1.00[ASW][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap]
rs11875065	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12456325	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12457923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12458365	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16954996	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34741369	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4797368	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs56349417	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57333366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57456386	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62087465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62087466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62087468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62087472	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62087494	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6506656	0.85[ASW][hapmap]
rs7229150	1.00[ASW][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7233757	0.89[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7243117	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes]
rs8088103	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8089405	0.83[EUR][1000 genomes]
rs8093378	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8093683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9676006	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9748497	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9748605	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv458023	chr18:9240413-9357786	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv576447	chr18:9240413-9357786	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv909365	chr18:9299538-9400422	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs16954989	TWSG1	cis	Esophagus Mucosa	GTEx
rs16954989	TWSG1	cis	multi-tissue	Pritchard
rs16954989	TWSG1	cis	Muscle Skeletal	GTEx
rs16954989	TWSG1	cis	Esophagus Muscularis	GTEx
rs16954989	TWSG1	cis	Thyroid	GTEx
rs16954989	TWSG1	cis	Artery Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9335400-9369400	Weak transcription	Pancreas	Pancrea
2	chr18:9335400-9371400	Weak transcription	Gastric	stomach
3	chr18:9335600-9366200	Weak transcription	Left Ventricle	heart
4	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr18:9335800-9357600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr18:9335800-9366200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
8	chr18:9335800-9367600	Weak transcription	Lung	lung
9	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
10	chr18:9336000-9355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr18:9336000-9366200	Weak transcription	Brain Angular Gyrus	brain
12	chr18:9336200-9361400	Weak transcription	Aorta	Aorta
13	chr18:9338200-9354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:9338400-9361600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr18:9338400-9366200	Weak transcription	Brain Anterior Caudate	brain
16	chr18:9338800-9366000	Weak transcription	Brain Hippocampus Middle	brain
17	chr18:9339600-9365600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr18:9341000-9371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr18:9341200-9361400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr18:9341200-9366400	Weak transcription	Brain Substantia Nigra	brain
21	chr18:9341200-9367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr18:9341200-9391400	Weak transcription	Liver	Liver
23	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:9341400-9366200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr18:9344000-9366000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr18:9344000-9367400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr18:9344200-9361400	Weak transcription	Brain Germinal Matrix	brain
28	chr18:9344200-9367600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr18:9344200-9367800	Weak transcription	Primary B cells from cord blood	blood
30	chr18:9344400-9360600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:9344400-9404200	Weak transcription	Primary T cells from cord blood	blood
32	chr18:9344800-9360200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr18:9345000-9361800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr18:9345200-9367400	Weak transcription	Fetal Brain Female	brain
35	chr18:9345600-9367000	Weak transcription	Fetal Intestine Large	intestine
36	chr18:9345600-9367400	Weak transcription	Placenta	Placenta
37	chr18:9345600-9377600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr18:9346600-9361400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr18:9346800-9361400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr18:9346800-9361400	Weak transcription	Fetal Muscle Leg	muscle
41	chr18:9348600-9359000	Weak transcription	Ovary	ovary
42	chr18:9348600-9360600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:9348600-9360600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr18:9348600-9361400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr18:9348600-9361400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr18:9348600-9362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr18:9348600-9365600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr18:9348600-9369600	Weak transcription	K562	blood
49	chr18:9348800-9354000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr18:9348800-9354000	Weak transcription	HSMMtube	muscle

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