Variant report

Variant	rs7548781
Chromosome Location	chr1:209915795-209915796
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PRDM1	chr1:209915786-209916124	Hela-S3	cervix:	n/a	chr1:209915948-209915962 chr1:209915949-209915958 chr1:209915947-209915962 chr1:209915949-209915962
2	POLR2A	chr1:209915722-209916044	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209913450..209916086-chr1:209919671..209921571,2	K562	blood:
2	chr1:209898728..209900231-chr1:209914075..209916050,2	K562	blood:

Variant related genes	Relation type
ENSG00000236136	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1000282	0.90[EUR][1000 genomes]
rs1000283	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10157973	0.90[CEU][hapmap]
rs10863783	0.91[EUR][1000 genomes]
rs10863785	0.91[EUR][1000 genomes]
rs11119327	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11119328	0.83[TSI][hapmap]
rs11119330	0.91[EUR][1000 genomes]
rs11119331	0.91[EUR][1000 genomes]
rs11119332	0.90[EUR][1000 genomes]
rs11119336	0.89[CEU][hapmap]
rs11485195	0.91[EUR][1000 genomes]
rs11487866	0.91[EUR][1000 genomes]
rs11487867	0.85[CEU][hapmap]
rs11807619	0.83[TSI][hapmap]
rs11808690	0.91[EUR][1000 genomes]
rs12034758	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs12059226	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12060420	0.91[EUR][1000 genomes]
rs12060922	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs12086634	0.91[EUR][1000 genomes]
rs12090931	0.91[EUR][1000 genomes]
rs12094117	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs12116437	0.91[EUR][1000 genomes]
rs12120361	0.95[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12129718	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12138452	0.91[EUR][1000 genomes]
rs1337531	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1415542	0.95[CEU][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1415544	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17389184	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs17389198	0.90[CEU][hapmap];0.80[EUR][1000 genomes]
rs1999826	0.83[EUR][1000 genomes]
rs2064148	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2205985	0.98[EUR][1000 genomes]
rs2236903	1.00[CEU][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2272867	0.90[CEU][hapmap];0.93[TSI][hapmap]
rs2282738	0.95[CEU][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2282739	1.00[CEU][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2282741	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2884090	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3765240	0.83[EUR][1000 genomes]
rs3766618	0.85[CEU][hapmap]
rs3766619	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs3817821	0.92[EUR][1000 genomes]
rs4314885	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4844891	1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627670	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs6540549	0.95[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs6540550	0.90[CEU][hapmap]
rs6540553	0.90[CEU][hapmap]
rs6665715	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs6672256	0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs667681	0.91[EUR][1000 genomes]
rs6679099	0.91[EUR][1000 genomes]
rs6679405	0.90[CEU][hapmap]
rs6702301	0.89[CEU][hapmap]
rs6752	0.91[EUR][1000 genomes]
rs7532324	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7539852	0.95[CEU][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs7555978	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs909710	0.90[CEU][hapmap];0.93[TSI][hapmap]
rs932335	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs9430012	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs9430014	0.91[EUR][1000 genomes]
rs9430015	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9430016	0.95[CEU][hapmap];0.94[TSI][hapmap];0.83[EUR][1000 genomes]
rs9430017	0.90[CEU][hapmap];0.80[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
rs7548781	SRGAP2	cis	parietal	SCAN
rs7548781	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	chr1:209914000-209917200	Enhancers	Liver	Liver
3	chr1:209914200-209916800	Enhancers	Fetal Intestine Large	intestine
4	chr1:209914200-209916800	Enhancers	Left Ventricle	heart
5	chr1:209914600-209915800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:209914600-209916600	Enhancers	Fetal Intestine Small	intestine
7	chr1:209914600-209917000	Enhancers	Ovary	ovary
8	chr1:209914800-209915800	Weak transcription	Right Ventricle	heart
9	chr1:209914800-209916200	Enhancers	Adipose Nuclei	Adipose
10	chr1:209914800-209917800	Enhancers	Pancreas	Pancrea
11	chr1:209914800-209917800	Enhancers	Right Atrium	heart
12	chr1:209915000-209916000	Enhancers	Brain Substantia Nigra	brain
13	chr1:209915000-209916400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:209915200-209916000	Enhancers	GM12878-XiMat	blood
15	chr1:209915200-209916200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:209915200-209916400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:209915200-209916400	Enhancers	Rectal Smooth Muscle	rectum
18	chr1:209915200-209916800	Enhancers	Fetal Stomach	stomach
19	chr1:209915200-209916800	Enhancers	Gastric	stomach
20	chr1:209915200-209917200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:209915200-209920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:209915200-209921000	Weak transcription	Spleen	Spleen
23	chr1:209915400-209915800	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr1:209915400-209916000	Active TSS	Rectal Mucosa Donor 29	rectum
25	chr1:209915400-209916200	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr1:209915400-209916600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:209915400-209917200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:209915400-209917600	Weak transcription	Lung	lung
29	chr1:209915400-209918600	Enhancers	Brain Angular Gyrus	brain
30	chr1:209915400-209920400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:209915400-209920800	Weak transcription	Esophagus	oesophagus
32	chr1:209915600-209915800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr1:209915600-209915800	Flanking Active TSS	Fetal Heart	heart
34	chr1:209915600-209916000	Active TSS	Brain Anterior Caudate	brain
35	chr1:209915600-209916000	Active TSS	Colon Smooth Muscle	Colon
36	chr1:209915600-209916000	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr1:209915600-209916000	Active TSS	NHLF	lung
38	chr1:209915600-209916200	Flanking Active TSS	Brain Hippocampus Middle	brain
39	chr1:209915600-209916200	Active TSS	Fetal Lung	lung
40	chr1:209915600-209916400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:209915600-209916400	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr1:209915600-209916400	Flanking Active TSS	Osteobl	bone
43	chr1:209915600-209920600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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