Variant report

Variant	rs10797988
Chromosome Location	chr1:184783699-184783700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10797989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10797990	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1857954	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2135737	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs338562	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs338563	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs338564	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap]
rs338565	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs338566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs338567	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs338568	1.00[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap]
rs338570	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4011648	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4011650	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4651234	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs520605	1.00[CEU][hapmap];0.95[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs521366	0.89[EUR][1000 genomes]
rs533853	0.86[EUR][1000 genomes]
rs543912	0.81[GIH][hapmap]
rs641337	0.81[GIH][hapmap]
rs6424964	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671637	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519082	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs906285	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];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	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv508677	chr1:184778620-184825302	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10797988	PRG4	cis	parietal	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184756800-184794000	Weak transcription	Thymus	Thymus
2	chr1:184762000-184787800	Weak transcription	Spleen	Spleen
3	chr1:184762400-184789400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:184762600-184792800	Weak transcription	Colonic Mucosa	Colon
5	chr1:184768000-184809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:184770800-184787000	Weak transcription	Gastric	stomach
7	chr1:184772000-184792000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:184772400-184801800	Weak transcription	Primary T cells from cord blood	blood
9	chr1:184772800-184790600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:184773200-184809400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:184775200-184787400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr1:184775400-184787800	Weak transcription	Esophagus	oesophagus
13	chr1:184775400-184791600	Weak transcription	Stomach Mucosa	stomach
14	chr1:184775600-184796800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:184775800-184784200	Weak transcription	Fetal Heart	heart
16	chr1:184775800-184794000	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:184777000-184792200	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:184777400-184791600	Weak transcription	Pancreas	Pancrea
19	chr1:184777600-184786800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:184777600-184787600	Weak transcription	Lung	lung
21	chr1:184777800-184787600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:184778000-184784400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:184778000-184787600	Weak transcription	Aorta	Aorta
24	chr1:184778000-184789400	Weak transcription	K562	blood
25	chr1:184778000-184791400	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:184778200-184787200	Weak transcription	Fetal Muscle Trunk	muscle
27	chr1:184780400-184787400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:184780400-184787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:184780400-184789400	Weak transcription	Fetal Stomach	stomach
30	chr1:184781200-184785400	Weak transcription	Right Ventricle	heart
31	chr1:184781200-184793400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:184781400-184786800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:184781400-184790000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:184781400-184792000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:184781600-184785200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
36	chr1:184781600-184790800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr1:184781600-184793400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:184782000-184784000	Weak transcription	Left Ventricle	heart
39	chr1:184782000-184786200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:184782000-184789800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr1:184782200-184784000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:184782600-184783800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr1:184782800-184784200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:184783000-184785400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:184783000-184787600	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:184783000-184807800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:184783200-184784200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:184783200-184786800	Weak transcription	Colon Smooth Muscle	Colon
49	chr1:184783200-184787000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:184783200-184787600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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