Variant report

Variant	rs3112270
Chromosome Location	chr3:112180644-112180645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13090873	0.86[ASN][1000 genomes]
rs1488257	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1488258	0.96[EUR][1000 genomes]
rs1879515	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1961790	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2633540	0.93[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633552	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633553	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633559	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633564	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2633565	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2633568	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2633569	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633586	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633587	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2633590	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2633610	0.91[EUR][1000 genomes]
rs2633611	0.91[EUR][1000 genomes]
rs2683910	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2683911	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2683912	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2683914	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2683915	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2683916	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705511	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705513	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705528	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2705529	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2705545	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2952322	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3109032	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3112271	0.96[EUR][1000 genomes]
rs35349813	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs721361	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721362	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs721363	0.96[EUR][1000 genomes]
rs7625194	0.84[ASN][1000 genomes]
rs939579	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs939580	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3112270	CD200	cis	lymphoblastoid	seeQTL

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112173400-112182200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:112176400-112180800	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr3:112177000-112181000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:112177800-112182200	Enhancers	Primary T cells from cord blood	blood
5	chr3:112179000-112184800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr3:112179200-112183600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:112179200-112184200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:112179400-112182000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:112179600-112180800	Enhancers	Primary B cells from cord blood	blood
10	chr3:112179800-112181600	Weak transcription	Fetal Thymus	thymus
11	chr3:112179800-112181800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:112179800-112181800	ZNF genes & repeats	GM12878-XiMat	blood
13	chr3:112179800-112189800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:112180000-112182000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:112180000-112182000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:112180200-112181600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:112180200-112181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr3:112180200-112181800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr3:112180200-112181800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:112180200-112181800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr3:112180200-112182000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr3:112180200-112182000	Weak transcription	Thymus	Thymus
23	chr3:112180400-112195400	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr3:112180600-112181600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:112180600-112182000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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