Variant report

Variant	rs3753383
Chromosome Location	chr1:160599652-160599653
allele	C/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: 13 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11265452	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs1503854	1.00[CHB][hapmap]
rs164283	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs16832283	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs2753260	0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs3753381	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	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670721	0.82[MEX][hapmap]
rs6697247	0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550771	0.89[CHD][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3753383	NCSTN	cis	cerebellum	SCAN
rs3753383	ADAMTS4	cis	cerebellum	SCAN
rs3753383	NHLH1	cis	cerebellum	SCAN
rs3753383	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs3753383	VANGL2	cis	cerebellum	SCAN
rs3753383	OLFML2B	cis	parietal	SCAN
rs3753383	THBS3	cis	cerebellum	SCAN
rs3753383	HCN3	cis	cerebellum	SCAN

Chromatin state (count:53 , 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	chr1:160597400-160599800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:160597400-160602400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:160598000-160600000	Flanking Active TSS	Dnd41	blood
12	chr1:160598000-160605200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:160598200-160600000	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr1:160598400-160599800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr1:160598400-160600200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
16	chr1:160598400-160600400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr1:160598400-160601400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:160598600-160599800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr1:160598600-160600200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:160598600-160600400	Enhancers	Spleen	Spleen
21	chr1:160598600-160601400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:160598600-160601800	Enhancers	Placenta	Placenta
23	chr1:160598800-160600000	Enhancers	Fetal Muscle Trunk	muscle
24	chr1:160598800-160600200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:160598800-160601200	Enhancers	Fetal Intestine Small	intestine
26	chr1:160599000-160600600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:160599000-160601200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:160599000-160612200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:160599200-160600000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:160599200-160600000	Enhancers	Fetal Muscle Leg	muscle
31	chr1:160599200-160600800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:160599200-160601400	Enhancers	K562	blood
33	chr1:160599400-160599800	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
34	chr1:160599400-160599800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr1:160599400-160599800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr1:160599400-160600000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr1:160599400-160600200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr1:160599400-160600400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:160599400-160600400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:160599400-160600600	Enhancers	Duodenum Mucosa	Duodenum
41	chr1:160599400-160600600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr1:160599400-160600800	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr1:160599400-160600800	Enhancers	Primary hematopoietic stem cells	blood
44	chr1:160599400-160601000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:160599400-160601000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr1:160599400-160601200	Enhancers	Fetal Intestine Large	intestine
47	chr1:160599600-160599800	Active TSS	Thymus	Thymus
48	chr1:160599600-160600000	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr1:160599600-160600200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr1:160599600-160600600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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