Variant report

Variant	rs9608956
Chromosome Location	chr22:30901592-30901593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1001409	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1008801	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11912737	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914168	1.00[JPT][hapmap]
rs12165604	0.86[EUR][1000 genomes]
rs12484688	1.00[JPT][hapmap]
rs13053262	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13053759	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13054004	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13054381	0.80[AMR][1000 genomes]
rs13750	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs16988720	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16988803	1.00[JPT][hapmap]
rs16988810	1.00[JPT][hapmap]
rs16988814	1.00[JPT][hapmap]
rs17670707	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17670808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17738527	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17738540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1807514	0.99[EUR][1000 genomes]
rs1859479	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1986969	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2023967	0.90[AMR][1000 genomes]
rs2189835	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2412989	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412990	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35102600	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35530794	0.91[ASN][1000 genomes]
rs35841307	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4602314	0.91[ASN][1000 genomes]
rs4820019	1.00[JPT][hapmap]
rs4820869	1.00[JPT][hapmap]
rs4820874	1.00[JPT][hapmap]
rs60308761	0.84[AMR][1000 genomes]
rs6518692	0.98[EUR][1000 genomes]
rs6518693	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518695	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6518698	0.97[EUR][1000 genomes]
rs7284873	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7285878	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7286523	0.91[ASN][1000 genomes]
rs7286807	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7287003	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7287135	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7287596	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7289277	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7289820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7289828	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7291870	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7292573	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737940	0.97[EUR][1000 genomes]
rs737942	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8136225	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8136992	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8137267	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8137718	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8138759	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8141108	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8141286	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8141318	0.91[ASN][1000 genomes]
rs8141428	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8141671	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs878306	0.97[EUR][1000 genomes]
rs886615	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886616	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886617	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9306262	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9606735	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9606736	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9606738	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9606739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9606744	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9606745	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9606746	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9606747	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9606749	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608935	0.91[ASN][1000 genomes]
rs9608936	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9608938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9608940	0.91[ASN][1000 genomes]
rs9608941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.91[ASN][1000 genomes]
rs9608942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9608944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9608955	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608960	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608964	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608966	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608967	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608968	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9608972	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	esv3413089	chr22:30888110-30921604	ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9608956	SEC14L4	cis	cerebellum	SCAN
rs9608956	DUSP18	cis	parietal	SCAN
rs9608956	SEC14L4	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30898200-30903600	Enhancers	HepG2	liver
2	chr22:30900200-30902000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr22:30900600-30902000	Active TSS	Hela-S3	cervix
4	chr22:30901200-30901600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
5	chr22:30901200-30901600	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr22:30901200-30901600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr22:30901200-30901600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr22:30901200-30901600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:30901200-30901600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr22:30901200-30901600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr22:30901200-30901600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr22:30901200-30901600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr22:30901200-30901600	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
14	chr22:30901200-30901600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
15	chr22:30901200-30901600	Bivalent Enhancer	Fetal Intestine Small	intestine
16	chr22:30901200-30901600	Flanking Active TSS	Gastric	stomach
17	chr22:30901200-30901600	Bivalent Enhancer	Ovary	ovary
18	chr22:30901200-30901600	Bivalent Enhancer	NHEK	skin
19	chr22:30901200-30901800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr22:30901200-30901800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr22:30901200-30901800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr22:30901200-30901800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr22:30901200-30901800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr22:30901200-30901800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr22:30901200-30901800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr22:30901200-30901800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr22:30901200-30901800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr22:30901200-30901800	Enhancers	Pancreas	Pancrea
29	chr22:30901200-30901800	Enhancers	Right Atrium	heart
30	chr22:30901200-30901800	Flanking Active TSS	HMEC	breast
31	chr22:30901200-30902000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr22:30901200-30902000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr22:30901200-30902000	Bivalent Enhancer	Placenta	Placenta
34	chr22:30901200-30902000	Active TSS	A549	lung
35	chr22:30901400-30901600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr22:30901400-30901600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr22:30901400-30901600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
38	chr22:30901400-30901600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr22:30901400-30901600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr22:30901400-30901600	Bivalent Enhancer	Adipose Nuclei	Adipose
41	chr22:30901400-30901600	Flanking Active TSS	Liver	Liver
42	chr22:30901400-30901600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
43	chr22:30901400-30901600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
44	chr22:30901400-30901600	Bivalent Enhancer	Fetal Heart	heart
45	chr22:30901400-30901600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
46	chr22:30901400-30901600	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
47	chr22:30901400-30901600	Bivalent Enhancer	Right Ventricle	heart
48	chr22:30901400-30901600	Bivalent Enhancer	Spleen	Spleen
49	chr22:30901400-30901800	Active TSS	Lung	lung
50	chr22:30901400-30902600	Enhancers	Esophagus	oesophagus

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