Variant report

Variant	rs4987306
Chromosome Location	chr1:169674445-169674446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169674141..169677050-chr1:169763005..169764633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000460	Chromatin interaction
ENSG00000171806	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10489181	0.86[EUR][1000 genomes]
rs1051091	0.85[CHB][hapmap]
rs10919232	0.82[EUR][1000 genomes]
rs10919233	0.82[EUR][1000 genomes]
rs11584020	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11588380	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12023614	0.88[EUR][1000 genomes]
rs12044082	0.86[EUR][1000 genomes]
rs12072966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076368	0.95[CHB][hapmap]
rs12087033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862661	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16862663	0.86[EUR][1000 genomes]
rs16862672	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1883228	0.90[CHB][hapmap]
rs1883229	0.95[CHB][hapmap]
rs2205847	0.90[CHB][hapmap]
rs2205849	0.95[CHB][hapmap]
rs2272818	0.82[EUR][1000 genomes]
rs2298899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2420504	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766129	0.90[CHB][hapmap]
rs3917405	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3917428	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3917430	0.95[CHB][hapmap]
rs3917432	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4656192	0.86[EUR][1000 genomes]
rs4656699	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656700	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656718	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs4987298	0.95[CHB][hapmap]
rs4987301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4987328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5356	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5359	0.95[CHB][hapmap]
rs5368	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57793783	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7418242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520701	0.82[EUR][1000 genomes]
rs7523319	0.82[EUR][1000 genomes]
rs7523520	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs964555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532586	chr1:169593222-169713184	Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv872539	chr1:169658586-169674590	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1009313	chr1:169661299-169680173	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv872541	chr1:169672360-169695815	Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169662400-169676000	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr1:169667600-169676800	Genic enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:169668000-169677400	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
4	chr1:169670600-169678000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
5	chr1:169671000-169675000	Genic enhancers	Monocytes-CD14+_RO01746	blood
6	chr1:169671200-169679400	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr1:169672600-169677400	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
8	chr1:169672600-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:169672800-169674600	Weak transcription	Spleen	Spleen
10	chr1:169672800-169676000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:169673200-169674600	Transcr. at gene 5' and 3'	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:169673200-169676800	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
13	chr1:169673200-169678400	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
14	chr1:169673400-169676600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
15	chr1:169673800-169674800	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
16	chr1:169673800-169675800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:169674000-169674800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:169674000-169675200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:169674000-169675600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:169674000-169675800	Weak transcription	GM12878-XiMat	blood
21	chr1:169674000-169676000	Strong transcription	Fetal Thymus	thymus
22	chr1:169674000-169676000	Weak transcription	Thymus	Thymus
23	chr1:169674000-169676200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:169674200-169675000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:169674400-169674600	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr1:169674400-169675000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr1:169674400-169675000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:169674400-169675800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:169674400-169678000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood

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