Variant report

Variant	rs6540549
Chromosome Location	chr1:209922668-209922669
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209921622..209924785-chr1:209954989..209957828,3	MCF-7	breast:
2	chr1:209920122..209922907-chr1:209973621..209976183,2	MCF-7	breast:
3	chr1:209921608..209924525-chr1:209928498..209931459,3	K562	blood:
4	chr1:209921083..209924525-chr1:209927225..209931869,7	K562	blood:

Variant related genes	Relation type
ENSG00000117595	Chromatin interaction
ENSG00000009790	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1000283	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs1007693	0.81[CEU][hapmap]
rs10157973	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11119327	0.90[CEU][hapmap]
rs11119336	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11119337	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes]
rs11119340	0.81[CEU][hapmap]
rs11487867	0.81[CEU][hapmap]
rs12030655	0.90[EUR][1000 genomes]
rs12034758	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs12059226	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs12060922	0.90[CEU][hapmap]
rs12094117	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs12120361	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs12129718	0.87[EUR][1000 genomes]
rs1337531	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1415542	0.90[CEU][hapmap];0.88[TSI][hapmap]
rs1415544	0.87[EUR][1000 genomes]
rs17389184	0.81[CEU][hapmap]
rs17389198	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs1999826	0.86[EUR][1000 genomes]
rs2064148	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2205985	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236903	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2272867	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs2282738	0.90[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2282739	0.95[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2282741	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2884090	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3765240	0.86[EUR][1000 genomes]
rs3766618	0.80[CEU][hapmap]
rs3766619	0.90[CEU][hapmap]
rs3817821	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4314885	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4844891	0.95[CEU][hapmap];0.84[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs627670	0.95[CEU][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6540550	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6540551	0.90[EUR][1000 genomes]
rs6540552	0.88[EUR][1000 genomes]
rs6540553	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6540554	0.81[CEU][hapmap];0.83[MKK][hapmap]
rs6665715	0.95[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs6672256	0.82[TSI][hapmap]
rs6679405	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6685077	0.84[MKK][hapmap]
rs6700223	0.92[AMR][1000 genomes]
rs6702301	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs679846	0.86[EUR][1000 genomes]
rs7521461	0.88[EUR][1000 genomes]
rs7532324	0.93[EUR][1000 genomes]
rs7539852	0.90[CEU][hapmap];0.85[TSI][hapmap]
rs7548781	0.95[CEU][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs7555978	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs909710	0.95[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs932335	0.90[CEU][hapmap]
rs9430012	0.90[CEU][hapmap]
rs9430015	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9430016	0.90[CEU][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs9430017	0.95[CEU][hapmap];0.88[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
rs6540549	HSD11B1	cis	cerebellum	SCAN
rs6540549	SRGAP2	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209919800-209923400	Enhancers	Fetal Intestine Small	intestine
2	chr1:209921400-209923400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr1:209921400-209923400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:209921400-209925200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:209921400-209929800	Weak transcription	Right Atrium	heart
6	chr1:209921400-209930000	Weak transcription	Right Ventricle	heart
7	chr1:209921600-209922800	Enhancers	GM12878-XiMat	blood
8	chr1:209921600-209923200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:209921600-209924800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:209921600-209926600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr1:209921600-209926600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:209921600-209926800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:209921800-209922800	Weak transcription	Liver	Liver
14	chr1:209921800-209924200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:209921800-209924200	Weak transcription	A549	lung
16	chr1:209921800-209924600	Enhancers	Primary T cells from cord blood	blood
17	chr1:209921800-209924600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:209921800-209924800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:209921800-209924800	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:209921800-209924800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:209921800-209925000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:209921800-209925400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:209921800-209925400	Weak transcription	K562	blood
24	chr1:209921800-209929600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:209921800-209930000	Weak transcription	Stomach Mucosa	stomach
26	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
28	chr1:209922000-209923800	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr1:209922000-209924200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr1:209922000-209924800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:209922000-209928800	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:209922200-209923800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:209922200-209924200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:209922200-209924800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:209922200-209925000	Weak transcription	Fetal Intestine Large	intestine
36	chr1:209922400-209924400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:209922400-209924800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr1:209922400-209924800	Weak transcription	Fetal Thymus	thymus
39	chr1:209922400-209924800	Weak transcription	Thymus	Thymus
40	chr1:209922400-209931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:209922600-209923000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:209922600-209923800	Weak transcription	Primary B cells from cord blood	blood

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