Variant report

Variant	rs3778894
Chromosome Location	chr7:38253923-38253924
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	chr7:38253002..38255460-chr7:38256658..38259135,2	K562	blood:
2	chr7:38246853..38248824-chr7:38252553..38254232,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1014136	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10224886	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10234310	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254082	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282163	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464362	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11766931	0.99[ASN][1000 genomes]
rs11773477	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12669726	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12670582	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17410426	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270165	0.99[ASN][1000 genomes]
rs2392540	0.99[ASN][1000 genomes]
rs28664954	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55915216	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56147907	0.99[ASN][1000 genomes]
rs56228793	0.98[ASN][1000 genomes]
rs60713125	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62443299	0.91[ASN][1000 genomes]
rs62443315	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9638935	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9639788	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9986766	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016355	chr7:38168232-38372719	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv830963	chr7:38172988-38344779	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758112	chr7:38218703-38523455	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	esv2759524	chr7:38218703-38523455	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv427776	chr7:38218703-38523455	Genic enhancers Transcr. at gene 5' and 3' Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv830964	chr7:38218708-38390518	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv1030349	chr7:38227528-38372719	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv538818	chr7:38227528-38372719	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv1025974	chr7:38227528-38503472	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	nsv538819	chr7:38227528-38503472	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv433041	chr7:38229107-38358728	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv433044	chr7:38238119-38358728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv932229	chr7:38248340-38727527	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38218600-38259200	Weak transcription	Colonic Mucosa	Colon
2	chr7:38220200-38254800	Weak transcription	Brain Hippocampus Middle	brain
3	chr7:38223600-38255600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr7:38228000-38256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:38228200-38254400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:38230200-38259200	Weak transcription	K562	blood
7	chr7:38232400-38255000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr7:38232800-38255200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr7:38232800-38256000	Weak transcription	Fetal Brain Male	brain
10	chr7:38236000-38254200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:38236000-38254600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr7:38236400-38254800	Weak transcription	Brain Germinal Matrix	brain
13	chr7:38236800-38254600	Weak transcription	Small Intestine	intestine
14	chr7:38236800-38261600	Weak transcription	HMEC	breast
15	chr7:38237000-38255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:38237200-38255600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr7:38237600-38258600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:38237800-38261600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:38238000-38257000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:38238000-38259200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr7:38238400-38255400	Weak transcription	Lung	lung
22	chr7:38238600-38254600	Weak transcription	NH-A	brain
23	chr7:38238600-38268800	Weak transcription	Esophagus	oesophagus
24	chr7:38239200-38254600	Weak transcription	Gastric	stomach
25	chr7:38239200-38254600	Weak transcription	NHLF	lung
26	chr7:38239200-38255600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr7:38239200-38256200	Weak transcription	Aorta	Aorta
28	chr7:38239400-38254800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:38239800-38254800	Weak transcription	Brain Substantia Nigra	brain
30	chr7:38239800-38256600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:38240000-38254600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr7:38240000-38254600	Weak transcription	Pancreas	Pancrea
33	chr7:38240000-38254600	Weak transcription	Psoas Muscle	Psoas
34	chr7:38240400-38254600	Weak transcription	Liver	Liver
35	chr7:38244000-38254400	Weak transcription	Placenta	Placenta
36	chr7:38245400-38255600	Weak transcription	HepG2	liver
37	chr7:38246600-38255600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr7:38247000-38255000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr7:38247000-38255000	Strong transcription	GM12878-XiMat	blood
40	chr7:38247400-38254600	Weak transcription	Fetal Intestine Small	intestine
41	chr7:38247400-38255400	Weak transcription	Fetal Brain Female	brain
42	chr7:38247800-38254000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr7:38247800-38254200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr7:38247800-38254600	Weak transcription	Ovary	ovary
45	chr7:38247800-38255200	Weak transcription	Brain Anterior Caudate	brain
46	chr7:38247800-38255400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr7:38248400-38254200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:38248400-38255200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr7:38248800-38255000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr7:38249000-38254200	Weak transcription	Stomach Mucosa	stomach

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