Variant report

Variant	rs3753389
Chromosome Location	chr1:160807153-160807154
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160805876..160808335-chr1:160811999..160814822,2	K562	blood:
2	chr1:160802328..160804621-chr1:160806389..160808035,2	K562	blood:
3	chr1:160806018..160807839-chr1:160809156..160811151,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11265493	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265496	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs11582719	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs11587898	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs1319651	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2139660	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2280415	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2779790	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779792	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2990702	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2990703	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766378	0.89[YRI][hapmap]
rs3766379	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656936	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656937	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656938	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483197	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs489651	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs491061	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs499721	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512525	0.96[CEU][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs535610	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs536906	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs537957	0.94[EUR][1000 genomes]
rs541834	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549565	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs578608	0.90[EUR][1000 genomes]
rs60755678	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671710	0.96[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs6682654	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7518342	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	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
2	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3753389	CD244	cis	lymphoblastoid	seeQTL
rs3753389	ISG20L2	cis	cerebellum	SCAN
rs3753389	CD5L	cis	parietal	SCAN
rs3753389	RXFP4	cis	parietal	SCAN
rs3753389	PPOX	cis	cerebellum	SCAN
rs3753389	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160793000-160811600	Weak transcription	Gastric	stomach
2	chr1:160793400-160807400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:160803000-160807600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160803200-160807600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:160803200-160812400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:160803400-160807400	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr1:160803600-160810000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:160804000-160807600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:160804400-160807600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:160804600-160807400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:160804800-160809600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:160805000-160809200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:160805000-160809400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr1:160805200-160809000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:160805400-160808000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:160805400-160808600	Enhancers	Primary hematopoietic stem cells	blood
17	chr1:160805600-160807600	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:160805600-160808000	Enhancers	Fetal Thymus	thymus
19	chr1:160805600-160809000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:160805600-160809000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:160805600-160809200	Enhancers	Primary B cells from cord blood	blood
22	chr1:160805600-160809200	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:160805800-160807200	Enhancers	Thymus	Thymus
24	chr1:160805800-160807400	Enhancers	GM12878-XiMat	blood
25	chr1:160805800-160807600	Enhancers	Dnd41	blood
26	chr1:160806000-160807800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:160806000-160807800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:160806000-160808400	Enhancers	HSMMtube	muscle
29	chr1:160806000-160809000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr1:160806200-160807200	Enhancers	Fetal Intestine Large	intestine
31	chr1:160806200-160807400	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr1:160806200-160807400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:160806200-160807800	Enhancers	Duodenum Mucosa	Duodenum
34	chr1:160806200-160808200	Enhancers	Placenta	Placenta
35	chr1:160806200-160808600	Enhancers	Spleen	Spleen
36	chr1:160806400-160808200	Enhancers	Fetal Heart	heart
37	chr1:160806400-160808400	Enhancers	Fetal Intestine Small	intestine
38	chr1:160806600-160807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr1:160806600-160807600	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:160806600-160807600	Weak transcription	Adipose Nuclei	Adipose
41	chr1:160806600-160807600	Weak transcription	Colonic Mucosa	Colon
42	chr1:160806600-160807600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr1:160806600-160808200	Enhancers	Fetal Muscle Leg	muscle
44	chr1:160806600-160810800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:160806800-160807200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr1:160806800-160807400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:160806800-160807600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:160806800-160807600	Enhancers	Right Atrium	heart
49	chr1:160806800-160807800	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:160806800-160808200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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