Variant report

Variant	rs2018904
Chromosome Location	chr10:27081902-27081903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10508721	0.90[YRI][hapmap]
rs12413383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12764628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12774231	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12776877	0.88[EUR][1000 genomes]
rs12779919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12780703	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16927334	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17669895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17747961	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17748178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094150	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2182294	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2182295	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35175791	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531360	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5010875	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5025734	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67940790	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs68021348	0.83[EUR][1000 genomes]
rs7091364	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7092571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7092950	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7096584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7916104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920164	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[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	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2018904	PDSS1	cis	cerebellum	SCAN
rs2018904	ABI1	cis	cerebellum	SCAN
rs2018904	LYZL2	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27044800-27082000	Weak transcription	Fetal Lung	lung
2	chr10:27051400-27082000	Weak transcription	Fetal Stomach	stomach
3	chr10:27069800-27084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:27070600-27082800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:27070800-27091800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr10:27071000-27082000	Weak transcription	Fetal Brain Male	brain
7	chr10:27071000-27083800	Weak transcription	Fetal Intestine Small	intestine
8	chr10:27071000-27084600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:27071200-27082000	Weak transcription	A549	lung
10	chr10:27071200-27089000	Weak transcription	Lung	lung
11	chr10:27071200-27089600	Weak transcription	Spleen	Spleen
12	chr10:27071400-27088600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:27073000-27087000	Weak transcription	Thymus	Thymus
14	chr10:27073000-27088200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr10:27074200-27082200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr10:27074800-27083200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr10:27074800-27091600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr10:27074800-27091800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr10:27075000-27087000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr10:27075000-27087000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr10:27075000-27089400	Weak transcription	Left Ventricle	heart
22	chr10:27075000-27091600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:27075000-27104600	Weak transcription	Esophagus	oesophagus
24	chr10:27075200-27088400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr10:27078800-27082800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr10:27079000-27082200	Weak transcription	Primary B cells from cord blood	blood
27	chr10:27079800-27082200	Weak transcription	Right Ventricle	heart
28	chr10:27079800-27085000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:27079800-27091800	Weak transcription	Fetal Heart	heart
30	chr10:27079800-27092200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr10:27080000-27082800	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr10:27080200-27082200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:27080400-27082600	Enhancers	Brain Substantia Nigra	brain
34	chr10:27080400-27082800	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr10:27080400-27083000	Enhancers	Brain Anterior Caudate	brain
36	chr10:27080600-27082600	Enhancers	Brain Hippocampus Middle	brain
37	chr10:27080600-27082800	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr10:27080600-27083200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr10:27080800-27082000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr10:27080800-27082200	Enhancers	Liver	Liver
41	chr10:27080800-27082400	Enhancers	Brain Angular Gyrus	brain
42	chr10:27080800-27082600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:27080800-27082600	Enhancers	GM12878-XiMat	blood
44	chr10:27080800-27082800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr10:27080800-27083600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr10:27080800-27092000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr10:27081000-27082200	Enhancers	Fetal Brain Female	brain
48	chr10:27081000-27082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr10:27081000-27082600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr10:27081200-27082200	Enhancers	Brain Germinal Matrix	brain

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