Variant report

Variant	rs7616420
Chromosome Location	chr3:111273532-111273533
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	chr3:111272610..111274604-chr8:128532692..128534798,3	MCF-7	breast:
2	chr3:111272648..111276502-chr8:128532438..128536275,5	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10511298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10934101	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11916952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12494356	0.84[ASN][1000 genomes]
rs13066911	0.88[ASN][1000 genomes]
rs1391356	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1497990	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1513323	0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1603687	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088468	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2276873	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs2399391	0.88[AFR][1000 genomes]
rs6764960	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6788797	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721336	0.85[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7619086	1.00[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7628253	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7653347	0.88[CEU][hapmap];0.87[GIH][hapmap]
rs883113	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs924262	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs968910	0.86[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.84[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	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
4	nsv3946	chr3:111236035-111283038	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	esv3366991	chr3:111273062-111276060	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111268000-111275000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:111268800-111275000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:111268800-111281400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:111269400-111273600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr3:111269800-111273600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:111269800-111289200	Weak transcription	Thymus	Thymus
7	chr3:111271600-111273800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr3:111271600-111273800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr3:111271600-111274400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:111271600-111274800	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr3:111271600-111275000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:111271600-111281000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:111271600-111286000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:111271600-111286200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:111271600-111286600	Weak transcription	Fetal Thymus	thymus
16	chr3:111272600-111273800	Weak transcription	Primary T cells from cord blood	blood
17	chr3:111272600-111274400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr3:111272600-111274400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:111273400-111273600	Strong transcription	Dnd41	blood

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