Variant report

Variant	rs6770144
Chromosome Location	chr3:111365168-111365169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs11914473	1.00[ASN][1000 genomes]
rs1513328	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16858327	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs16858329	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16858353	0.88[CHD][hapmap]
rs17423232	0.81[TSI][hapmap]
rs2895386	0.99[ASN][1000 genomes]
rs3733176	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56172864	1.00[ASN][1000 genomes]
rs56306480	1.00[ASN][1000 genomes]
rs57067927	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57501419	0.98[ASN][1000 genomes]
rs57831621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763322	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765832	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6768092	1.00[ASN][1000 genomes]
rs6770679	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771309	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780210	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780729	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787870	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6801876	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230132	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230143	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73852844	1.00[ASN][1000 genomes]
rs73852849	1.00[ASN][1000 genomes]
rs7431849	0.83[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7637536	0.88[ASN][1000 genomes]
rs9819529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858544	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6770144	CD200	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111347000-111367200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:111347600-111367800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:111357000-111368800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:111358400-111366800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:111358400-111369400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:111358600-111367000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:111358800-111365600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:111358800-111367000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:111358800-111368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:111358800-111368600	Weak transcription	Thymus	Thymus
11	chr3:111359000-111366000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:111359000-111366200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:111359000-111368200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:111359200-111368400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:111361600-111366200	Weak transcription	Fetal Thymus	thymus
16	chr3:111362400-111366800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr3:111363200-111374600	Strong transcription	Primary T cells from cord blood	blood
18	chr3:111363600-111365400	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:111364600-111374200	Strong transcription	Dnd41	blood
20	chr3:111364600-111374600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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