Variant report

Variant	rs3753381
Chromosome Location	chr1:160599410-160599411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160598662..160600370-chr1:160606514..160608049,2	K562	blood:
2	chr1:160598148..160600427-chr1:160603712..160606354,2	MCF-7	breast:
3	chr1:160591264..160593776-chr1:160598506..160600175,2	K562	blood:
4	chr1:160589254..160593885-chr1:160595406..160601586,7	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11265452	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs11585738	0.86[MEX][hapmap]
rs12733256	0.86[ASN][1000 genomes]
rs1503854	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs164283	1.00[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs16832283	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap];0.86[ASN][1000 genomes]
rs17381453	0.86[MEX][hapmap]
rs2753260	0.86[MEX][hapmap]
rs3733264	0.86[MEX][hapmap]
rs3733265	0.86[MEX][hapmap]
rs3753383	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3753384	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6670721	0.80[MEX][hapmap]
rs6697247	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7550771	0.86[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3753381	CD84	cis	lymphoblastoid	seeQTL
rs3753381	VANGL2	cis	cerebellum	SCAN
rs3753381	NOS1AP	cis	parietal	SCAN
rs3753381	THBS3	cis	cerebellum	SCAN
rs3753381	HCN3	cis	cerebellum	SCAN
rs3753381	OLFML2B	cis	parietal	SCAN
rs3753381	NHLH1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160591800-160605200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
2	chr1:160592800-160601400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:160594600-160601200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:160595000-160601400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:160595400-160611000	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr1:160595600-160600000	Weak transcription	Small Intestine	intestine
7	chr1:160596800-160604000	Weak transcription	Lung	lung
8	chr1:160596800-160608400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:160597400-160599600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:160597400-160599800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:160597400-160602400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:160598000-160600000	Flanking Active TSS	Dnd41	blood
13	chr1:160598000-160605200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:160598200-160600000	Flanking Active TSS	Primary T cells from cord blood	blood
15	chr1:160598400-160599800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr1:160598400-160600200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
17	chr1:160598400-160600400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160598400-160601400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:160598600-160599800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
20	chr1:160598600-160600200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:160598600-160600400	Enhancers	Spleen	Spleen
22	chr1:160598600-160601400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr1:160598600-160601800	Enhancers	Placenta	Placenta
24	chr1:160598800-160600000	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:160598800-160600200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:160598800-160601200	Enhancers	Fetal Intestine Small	intestine
27	chr1:160599000-160600600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:160599000-160601200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:160599000-160612200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:160599200-160599600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:160599200-160600000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:160599200-160600000	Enhancers	Fetal Muscle Leg	muscle
33	chr1:160599200-160600800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr1:160599200-160601400	Enhancers	K562	blood
35	chr1:160599400-160599600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr1:160599400-160599600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr1:160599400-160599600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:160599400-160599600	Flanking Active TSS	Thymus	Thymus
39	chr1:160599400-160599800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
40	chr1:160599400-160599800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:160599400-160599800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr1:160599400-160600000	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr1:160599400-160600200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr1:160599400-160600400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:160599400-160600400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:160599400-160600600	Enhancers	Duodenum Mucosa	Duodenum
47	chr1:160599400-160600600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
48	chr1:160599400-160600800	Enhancers	Primary neutrophils fromperipheralblood	blood
49	chr1:160599400-160600800	Enhancers	Primary hematopoietic stem cells	blood
50	chr1:160599400-160601000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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