Variant report

Variant	rs3754021
Chromosome Location	chr1:92158751-92158752
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	chr1:92154030..92157001-chr1:92158555..92160542,2	K562	blood:
2	chr1:92156294..92159210-chr1:92161380..92163036,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10782997	0.82[CHD][hapmap];0.92[JPT][hapmap]
rs11165279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11165306	0.92[JPT][hapmap]
rs11165307	0.92[JPT][hapmap]
rs11165313	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12082710	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs12117058	0.92[JPT][hapmap]
rs12133463	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141338	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1805113	0.88[CHD][hapmap];0.92[JPT][hapmap]
rs2291477	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2296621	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[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765890	0.85[CEU][hapmap]
rs3767574	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6604050	0.92[JPT][hapmap]
rs7521418	0.92[JPT][hapmap]
rs7521726	0.92[JPT][hapmap]
rs7524066	0.86[CHD][hapmap];0.88[GIH][hapmap]
rs7530435	0.92[JPT][hapmap]
rs7549755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3754021	BTBD8	cis	parietal	SCAN
rs3754021	GBP5	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92145200-92159000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr1:92146800-92163000	Weak transcription	Hela-S3	cervix
3	chr1:92147400-92164600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:92149000-92170000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:92149400-92159000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:92149400-92172800	Weak transcription	Esophagus	oesophagus
7	chr1:92149600-92166000	Weak transcription	NHEK	skin
8	chr1:92150400-92158800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:92150400-92162600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr1:92150600-92159000	Weak transcription	Osteobl	bone
11	chr1:92150800-92159000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:92150800-92159000	Weak transcription	Stomach Mucosa	stomach
13	chr1:92150800-92160400	Weak transcription	K562	blood
14	chr1:92151200-92162400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:92151200-92164200	Weak transcription	Right Ventricle	heart
16	chr1:92151200-92172800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:92151400-92159000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:92151400-92162200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:92151600-92161800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:92151600-92162200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:92151600-92162200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:92151800-92162400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr1:92152400-92162400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:92152600-92159000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:92152600-92184200	Strong transcription	HepG2	liver
26	chr1:92152800-92162400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:92152800-92162400	Weak transcription	Left Ventricle	heart
28	chr1:92152800-92163200	Weak transcription	Fetal Heart	heart
29	chr1:92153000-92162400	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:92153000-92197000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr1:92153400-92159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:92154000-92162200	Weak transcription	Fetal Intestine Small	intestine
33	chr1:92154600-92159000	Weak transcription	NHLF	lung
34	chr1:92154800-92159200	Weak transcription	Lung	lung
35	chr1:92155400-92161600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:92155400-92162400	Weak transcription	Spleen	Spleen
37	chr1:92155400-92178800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:92155600-92178800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:92155800-92159000	Weak transcription	Aorta	Aorta
40	chr1:92155800-92162000	Weak transcription	Fetal Intestine Large	intestine
41	chr1:92155800-92171600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:92155800-92191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:92156000-92159000	Weak transcription	Pancreas	Pancrea
44	chr1:92156000-92161400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:92156000-92163200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr1:92156000-92163200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:92156000-92172800	Weak transcription	Gastric	stomach
48	chr1:92156200-92158800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:92156200-92162400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:92156200-92172800	Weak transcription	Rectal Mucosa Donor 29	rectum

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