Variant report

Variant	rs12967229
Chromosome Location	chr18:9366501-9366502
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:9366182..9367790-chr18:9474261..9475962,2	MCF-7	breast:
2	chr18:9366198..9366924-chr18:9516202..9517058,2	MCF-7	breast:
3	chr18:9359169..9361236-chr18:9364960..9366916,2	K562	blood:

Variant related genes	Relation type
ENSG00000017797	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1062359	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1074159	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10853376	0.86[ASN][1000 genomes]
rs11081473	0.87[ASN][1000 genomes]
rs11081474	0.88[ASN][1000 genomes]
rs11663997	0.84[EUR][1000 genomes]
rs11873989	0.88[ASN][1000 genomes]
rs11875585	0.86[ASN][1000 genomes]
rs11875640	0.86[ASN][1000 genomes]
rs11876171	0.86[ASN][1000 genomes]
rs11876202	0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs11878159	0.96[ASN][1000 genomes]
rs11878163	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12052039	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12604438	0.87[ASN][1000 genomes]
rs12956692	0.84[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12959183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12962014	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12962166	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12963151	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13285	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1443594	0.86[ASN][1000 genomes]
rs1443595	0.86[ASN][1000 genomes]
rs1443599	0.88[ASN][1000 genomes]
rs1605473	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1605474	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1605476	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2028655	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2048146	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2120317	0.87[ASN][1000 genomes]
rs2298545	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs35584133	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3786173	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs3859293	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs4567794	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4797366	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4798794	0.86[ASN][1000 genomes]
rs4798797	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4798801	0.95[ASN][1000 genomes]
rs4798802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4798804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4798805	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4798806	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4798808	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57524426	0.86[ASN][1000 genomes]
rs62087478	0.96[ASN][1000 genomes]
rs6506652	0.86[ASN][1000 genomes]
rs6506653	0.86[ASN][1000 genomes]
rs6506654	0.89[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs6506655	0.98[ASN][1000 genomes]
rs6506661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs66827086	0.81[EUR][1000 genomes]
rs7228819	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7230171	0.96[ASN][1000 genomes]
rs7230328	0.96[ASN][1000 genomes]
rs7233751	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7233925	0.86[ASN][1000 genomes]
rs7234330	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7234762	0.85[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs7236073	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7236396	0.96[ASN][1000 genomes]
rs7237136	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7237485	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7237850	0.82[ASN][1000 genomes]
rs7239225	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7240798	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7242488	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7243376	0.96[ASN][1000 genomes]
rs7244054	0.95[ASN][1000 genomes]
rs7245034	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72948167	0.95[ASN][1000 genomes]
rs7846	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8085920	0.86[ASN][1000 genomes]
rs8085947	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8087892	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs8093045	0.96[ASN][1000 genomes]
rs8095060	0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs8096911	0.88[ASN][1000 genomes]
rs8096988	0.86[ASN][1000 genomes]
rs8097654	0.88[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs8097838	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8099673	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs925100	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs9635818	0.84[ASN][1000 genomes]
rs9635819	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs9635873	0.84[ASN][1000 genomes]
rs965280	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9675975	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9944562	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9956536	0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9957701	0.84[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9959183	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9963516	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9966961	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9967388	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12967229	TWSG1	cis	multi-tissue	Pritchard

Chromatin state (count:100 , 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	chr18:9335600-9372600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:9335800-9367600	Weak transcription	Fetal Thymus	thymus
5	chr18:9335800-9367600	Weak transcription	Lung	lung
6	chr18:9335800-9370200	Weak transcription	Adipose Nuclei	Adipose
7	chr18:9341000-9371800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr18:9341200-9367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr18:9341200-9391400	Weak transcription	Liver	Liver
10	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr18:9344000-9367400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr18:9344200-9367600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr18:9344200-9367800	Weak transcription	Primary B cells from cord blood	blood
14	chr18:9344400-9404200	Weak transcription	Primary T cells from cord blood	blood
15	chr18:9345200-9367400	Weak transcription	Fetal Brain Female	brain
16	chr18:9345600-9367000	Weak transcription	Fetal Intestine Large	intestine
17	chr18:9345600-9367400	Weak transcription	Placenta	Placenta
18	chr18:9345600-9377600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr18:9348600-9369600	Weak transcription	K562	blood
20	chr18:9348800-9367400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr18:9348800-9367600	Weak transcription	NHDF-Ad	bronchial
22	chr18:9349000-9367400	Weak transcription	Dnd41	blood
23	chr18:9354400-9380400	Weak transcription	NHLF	lung
24	chr18:9358800-9367400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr18:9359400-9369200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr18:9359600-9369200	Weak transcription	Spleen	Spleen
27	chr18:9360400-9403000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr18:9360600-9374000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr18:9361400-9366600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr18:9361600-9369000	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr18:9361800-9380200	Weak transcription	Small Intestine	intestine
32	chr18:9362000-9367200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr18:9362000-9367200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr18:9362000-9367400	Weak transcription	Fetal Lung	lung
35	chr18:9362000-9369600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:9362000-9380400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr18:9362200-9367400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr18:9362400-9380000	Weak transcription	Brain Germinal Matrix	brain
39	chr18:9362600-9366600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr18:9362800-9369200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr18:9362800-9374400	Weak transcription	Primary B cells from peripheral blood	blood
42	chr18:9363200-9367400	Weak transcription	Fetal Intestine Small	intestine
43	chr18:9363200-9369600	Weak transcription	A549	lung
44	chr18:9363200-9369800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr18:9363200-9380200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr18:9363400-9369400	Weak transcription	Fetal Heart	heart
47	chr18:9363600-9367200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr18:9363600-9367400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr18:9364000-9366600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr18:9364200-9370200	Strong transcription	Fetal Stomach	stomach

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