Variant report

Variant	rs10489342
Chromosome Location	chr1:209935778-209935779
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:209935010..209937588-chr1:209955355..209957792,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1007693	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10157973	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10863786	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11119336	0.84[CEU][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs11119337	0.92[EUR][1000 genomes]
rs11119338	0.89[JPT][hapmap]
rs11119340	0.86[CEU][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs11119341	0.81[CEU][hapmap];0.89[JPT][hapmap]
rs12030655	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12034758	0.82[ASN][1000 genomes]
rs12059226	0.82[MEX][hapmap]
rs12079960	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12094117	0.82[MEX][hapmap]
rs12120361	0.82[MEX][hapmap]
rs1415542	0.82[MEX][hapmap]
rs17015169	0.86[ASW][hapmap];0.86[CEU][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17389198	0.81[CEU][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1999826	0.96[ASN][1000 genomes]
rs2076150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272867	0.81[CEU][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs3753606	0.86[ASW][hapmap];0.95[CEU][hapmap];0.80[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3765240	0.96[ASN][1000 genomes]
rs611861	0.91[CEU][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs627670	0.81[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs643118	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540549	0.84[MKK][hapmap]
rs6540550	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540551	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540552	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540553	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6540554	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540555	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6540556	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs654984	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6665715	0.81[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6672256	0.82[MEX][hapmap]
rs6679405	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6679631	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6685077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691905	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6696463	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6700223	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6702301	0.80[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs679846	0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7521461	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7536882	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7548219	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs909710	0.81[CEU][hapmap];0.89[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[ASN][1000 genomes]
rs9430016	0.94[MEX][hapmap]
rs9430017	0.81[CEU][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
6	nsv4343	chr1:209929932-209974877	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv3453470	chr1:209935214-209936154	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
8	esv3346697	chr1:209935230-209935865	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
9	esv3517539	chr1:209935246-209936157	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
10	esv3517541	chr1:209935273-209936130	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
11	esv3517542	chr1:209935277-209936126	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	esv3453469	chr1:209935322-209936081	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	esv3517538	chr1:209935332-209936082	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
14	nsv159698	chr1:209935336-209936076	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
15	esv3453471	chr1:209935336-209936080	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
16	esv3517543	chr1:209935336-209936080	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10489342	HSD11B1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209921800-209940800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209921800-209942000	Weak transcription	Pancreas	Pancrea
3	chr1:209930800-209938800	Weak transcription	Fetal Intestine Large	intestine
4	chr1:209931000-209941800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:209931000-209942000	Weak transcription	Esophagus	oesophagus
6	chr1:209931000-209943200	Weak transcription	Lung	lung
7	chr1:209931000-209943600	Weak transcription	Gastric	stomach
8	chr1:209931800-209935800	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr1:209931800-209940600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:209932000-209936800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:209932200-209941200	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr1:209932200-209941400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:209932200-209941800	Weak transcription	Colonic Mucosa	Colon
14	chr1:209932200-209942000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:209932600-209936000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:209932600-209937800	Strong transcription	Dnd41	blood
17	chr1:209932600-209940000	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:209932800-209938000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr1:209932800-209939400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:209933000-209937800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:209933000-209940000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:209933000-209940800	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr1:209933200-209936200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:209933200-209939400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:209933200-209939400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:209933400-209939400	Strong transcription	Thymus	Thymus
27	chr1:209933400-209940600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:209933600-209937800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:209933600-209940800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr1:209933800-209938000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr1:209933800-209939200	Weak transcription	Fetal Intestine Small	intestine
32	chr1:209933800-209941600	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:209934000-209941600	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:209934400-209937800	Genic enhancers	Monocytes-CD14+_RO01746	blood
35	chr1:209934600-209941600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr1:209934800-209937800	Strong transcription	GM12878-XiMat	blood
37	chr1:209934800-209939200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:209934800-209940600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:209934800-209941800	Weak transcription	Right Ventricle	heart
40	chr1:209934800-209942000	Weak transcription	Brain Substantia Nigra	brain
41	chr1:209934800-209942000	Weak transcription	Right Atrium	heart
42	chr1:209935000-209940600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr1:209935200-209937800	Strong transcription	Primary hematopoietic stem cells	blood
44	chr1:209935200-209938200	Strong transcription	Primary B cells from cord blood	blood
45	chr1:209935200-209940600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:209935400-209937000	Strong transcription	Spleen	Spleen
47	chr1:209935400-209937800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:209935400-209938800	Genic enhancers	Primary T cells from cord blood	blood
49	chr1:209935400-209939200	Strong transcription	Fetal Thymus	thymus
50	chr1:209935600-209936600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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