Variant report

Variant	rs3817821
Chromosome Location	chr1:209918503-209918504
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HSD11B1-1	chr1:209917718-209918559	NONHSAT009230

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1000282	0.83[EUR][1000 genomes]
rs1000283	0.95[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs10157973	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs10863783	0.84[EUR][1000 genomes]
rs10863785	0.84[EUR][1000 genomes]
rs11119327	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs11119330	0.84[EUR][1000 genomes]
rs11119331	0.84[EUR][1000 genomes]
rs11119332	0.83[EUR][1000 genomes]
rs11119336	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs11119337	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11485195	0.84[EUR][1000 genomes]
rs11487866	0.84[EUR][1000 genomes]
rs11487867	0.85[CEU][hapmap]
rs11808690	0.84[EUR][1000 genomes]
rs12030655	0.85[EUR][1000 genomes]
rs12034758	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs12059226	0.95[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs12060420	0.84[EUR][1000 genomes]
rs12060922	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs12086634	0.84[EUR][1000 genomes]
rs12090931	0.84[EUR][1000 genomes]
rs12094117	0.95[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs12116437	0.84[EUR][1000 genomes]
rs12120361	0.95[CEU][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs12129718	0.92[EUR][1000 genomes]
rs12138452	0.84[EUR][1000 genomes]
rs1337531	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1415542	0.95[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs1415544	0.92[EUR][1000 genomes]
rs17389184	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs17389198	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1999826	0.92[EUR][1000 genomes]
rs2064148	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2205985	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2236903	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2272867	0.90[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2282738	0.80[ASW][hapmap];0.95[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2282739	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2282741	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2884090	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3765240	0.92[EUR][1000 genomes]
rs3766618	0.85[CEU][hapmap]
rs3766619	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs4314885	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4844891	0.80[ASW][hapmap];1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs627670	0.90[CEU][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6540549	0.92[ASW][hapmap];0.95[CEU][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6540550	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6540551	0.85[EUR][1000 genomes]
rs6540552	0.83[EUR][1000 genomes]
rs6540553	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6540554	0.89[MKK][hapmap]
rs6665715	0.90[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs6672256	0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs667681	0.84[EUR][1000 genomes]
rs6679099	0.84[EUR][1000 genomes]
rs6679405	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs6685077	0.91[MKK][hapmap]
rs6700223	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6702301	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs6752	0.84[EUR][1000 genomes]
rs679846	0.82[EUR][1000 genomes]
rs7521461	0.83[EUR][1000 genomes]
rs7532324	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539852	0.95[CEU][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7548781	1.00[CEU][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs7555978	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs909710	0.90[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs932335	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9430012	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs9430014	0.84[EUR][1000 genomes]
rs9430015	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9430016	0.95[CEU][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs9430017	0.90[CEU][hapmap];0.84[EUR][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	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3817821	SRGAP2	cis	parietal	SCAN
rs3817821	HSD11B1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209907600-209920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209915200-209920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:209915200-209921000	Weak transcription	Spleen	Spleen
4	chr1:209915400-209918600	Enhancers	Brain Angular Gyrus	brain
5	chr1:209915400-209920400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:209915400-209920800	Weak transcription	Esophagus	oesophagus
7	chr1:209915600-209920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:209915800-209919800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:209916000-209920800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:209916000-209920800	Weak transcription	GM12878-XiMat	blood
11	chr1:209916200-209919800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:209916200-209920200	Weak transcription	Adipose Nuclei	Adipose
13	chr1:209916400-209918800	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:209916600-209918800	Enhancers	Brain Substantia Nigra	brain
15	chr1:209916600-209919800	Weak transcription	Fetal Intestine Small	intestine
16	chr1:209916800-209919400	Weak transcription	Fetal Intestine Large	intestine
17	chr1:209916800-209920400	Weak transcription	Gastric	stomach
18	chr1:209916800-209920800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:209916800-209920800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:209916800-209920800	Weak transcription	Left Ventricle	heart
21	chr1:209917000-209920400	Weak transcription	Ovary	ovary
22	chr1:209917000-209920400	Weak transcription	HMEC	breast
23	chr1:209917000-209920600	Weak transcription	Brain Anterior Caudate	brain
24	chr1:209917000-209920800	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:209917000-209920800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:209917200-209919400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:209917200-209919600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:209917200-209920400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:209917200-209920600	Weak transcription	Osteobl	bone
30	chr1:209917200-209920800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:209917200-209920800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:209917200-209920800	Weak transcription	Liver	Liver
33	chr1:209917200-209920800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:209917200-209920800	Weak transcription	NH-A	brain
35	chr1:209917200-209920800	Weak transcription	NHLF	lung
36	chr1:209917800-209918800	Enhancers	Brain Cingulate Gyrus	brain
37	chr1:209917800-209919000	Enhancers	Brain Hippocampus Middle	brain
38	chr1:209917800-209919200	Weak transcription	Lung	lung
39	chr1:209917800-209919600	Weak transcription	Fetal Heart	heart
40	chr1:209917800-209920800	Weak transcription	Pancreas	Pancrea
41	chr1:209917800-209920800	Weak transcription	Right Atrium	heart
42	chr1:209917800-209920800	Weak transcription	Right Ventricle	heart
43	chr1:209918400-209920800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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