Variant report

Variant	rs6682654
Chromosome Location	chr1:160809003-160809004
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr1:160808718-160809089	GM12878	blood:	n/a	n/a
2	RUNX3	chr1:160808571-160809072	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CD244	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11265493	0.84[CEU][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs11265496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265498	0.82[MKK][hapmap]
rs11582719	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11587898	1.00[CEU][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1319651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2139660	0.84[CEU][hapmap]
rs2280415	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2779790	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2779792	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2990702	0.98[EUR][1000 genomes]
rs2990703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753389	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs3766379	0.96[CEU][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs4656937	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs4656938	0.96[CEU][hapmap];0.98[TSI][hapmap];0.95[EUR][1000 genomes]
rs483197	0.97[EUR][1000 genomes]
rs489651	1.00[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs491061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499721	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs512525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs535610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536906	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537957	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541834	0.98[EUR][1000 genomes]
rs549565	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[EUR][1000 genomes]
rs578608	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60755678	0.92[EUR][1000 genomes]
rs6671710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518342	0.84[CEU][hapmap];0.86[AMR][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6682654	CD244	cis	lymphoblastoid	seeQTL
rs6682654	CD244	cis	multi-tissue	Pritchard
rs6682654	ISG20L2	cis	cerebellum	SCAN
rs6682654	RXFP4	cis	parietal	SCAN
rs6682654	PPOX	cis	cerebellum	SCAN
rs6682654	CD244	cis	Lymphoblastoid	GTEx
rs6682654	CD244	Cis_1M	lymphoblastoid	RTeQTL
rs6682654	CD5L	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160793000-160811600	Weak transcription	Gastric	stomach
2	chr1:160803200-160812400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:160803600-160810000	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr1:160804800-160809600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:160805000-160809200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr1:160805000-160809400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr1:160805600-160809200	Enhancers	Primary B cells from cord blood	blood
8	chr1:160805600-160809200	Enhancers	Primary B cells from peripheral blood	blood
9	chr1:160806600-160810800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:160806800-160809800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:160807200-160811000	Weak transcription	Fetal Intestine Large	intestine
12	chr1:160807800-160809200	Genic enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:160807800-160809400	Weak transcription	Adipose Nuclei	Adipose
14	chr1:160808000-160809800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:160808200-160809200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:160808200-160811800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:160808200-160812200	Weak transcription	Fetal Heart	heart
18	chr1:160808400-160810400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:160808400-160811000	Weak transcription	Fetal Intestine Small	intestine
20	chr1:160808600-160810600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:160808600-160811000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr1:160808600-160811000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr1:160808600-160812600	Genic enhancers	Primary hematopoietic stem cells	blood
24	chr1:160808800-160810200	Enhancers	Primary T cells from cord blood	blood
25	chr1:160808800-160811600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:160808800-160812600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:160809000-160809200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:160809000-160810200	Enhancers	Fetal Thymus	thymus
29	chr1:160809000-160810200	Enhancers	Dnd41	blood
30	chr1:160809000-160810600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:160809000-160810600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr1:160809000-160810800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr1:160809000-160811200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr1:160809000-160812400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr1:160809000-160812800	Enhancers	Thymus	Thymus
36	chr1:160809000-160813600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:160809000-160813600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:160809000-160814200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr1:160809000-160814400	Weak transcription	Spleen	Spleen

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