Variant report

Variant	rs2280415
Chromosome Location	chr1:160806611-160806612
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	chr1:160748693..160751200-chr1:160804767..160806895,2	MCF-7	breast:
3	chr1:160802328..160804621-chr1:160806389..160808035,2	K562	blood:
4	chr1:160806018..160807839-chr1:160809156..160811151,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11265493	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265496	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11582719	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11587898	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1319651	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2139660	0.89[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779790	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779792	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2990702	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2990703	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3753389	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]
rs3766379	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656936	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4656937	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656938	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483197	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs489651	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs491061	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs499721	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512525	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs535610	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs536906	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs537957	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs541834	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549565	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs578608	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60755678	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6671710	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6682654	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7518342	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2280415	CD244	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 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	chr1:160805000-160807000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:160805000-160809200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:160805000-160809400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr1:160805200-160809000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:160805400-160808000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:160805400-160808600	Enhancers	Primary hematopoietic stem cells	blood
18	chr1:160805600-160807600	Enhancers	Primary T cells fromperipheralblood	blood
19	chr1:160805600-160808000	Enhancers	Fetal Thymus	thymus
20	chr1:160805600-160809000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:160805600-160809000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:160805600-160809200	Enhancers	Primary B cells from cord blood	blood
23	chr1:160805600-160809200	Enhancers	Primary B cells from peripheral blood	blood
24	chr1:160805800-160807200	Enhancers	Thymus	Thymus
25	chr1:160805800-160807400	Enhancers	GM12878-XiMat	blood
26	chr1:160805800-160807600	Enhancers	Dnd41	blood
27	chr1:160806000-160807800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:160806000-160807800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:160806000-160808400	Enhancers	HSMMtube	muscle
30	chr1:160806000-160809000	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:160806200-160807200	Enhancers	Fetal Intestine Large	intestine
32	chr1:160806200-160807400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr1:160806200-160807400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:160806200-160807800	Enhancers	Duodenum Mucosa	Duodenum
35	chr1:160806200-160808200	Enhancers	Placenta	Placenta
36	chr1:160806200-160808600	Enhancers	Spleen	Spleen
37	chr1:160806400-160806800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
38	chr1:160806400-160806800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:160806400-160807000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr1:160806400-160807000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr1:160806400-160808200	Enhancers	Fetal Heart	heart
42	chr1:160806400-160808400	Enhancers	Fetal Intestine Small	intestine
43	chr1:160806600-160806800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:160806600-160807000	Enhancers	Brain Substantia Nigra	brain
45	chr1:160806600-160807000	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr1:160806600-160807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr1:160806600-160807600	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr1:160806600-160807600	Weak transcription	Adipose Nuclei	Adipose
49	chr1:160806600-160807600	Weak transcription	Colonic Mucosa	Colon
50	chr1:160806600-160807600	Enhancers	Rectal Mucosa Donor 29	rectum

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