Variant report

Variant	rs3776789
Chromosome Location	chr5:52328960-52328961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52319764..52321344-chr5:52327151..52329228,2	K562	blood:
2	chr5:52313064..52315275-chr5:52327348..52329688,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10041086	0.92[ASN][1000 genomes]
rs11741738	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1445941	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1445942	0.80[AMR][1000 genomes]
rs17298242	0.82[AMR][1000 genomes]
rs1900182	0.83[AMR][1000 genomes]
rs2075614	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2287950	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303124	0.83[AMR][1000 genomes]
rs3212430	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3212433	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212435	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212436	0.92[ASN][1000 genomes]
rs3212446	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212483	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212537	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3212556	0.97[ASN][1000 genomes]
rs3212603	0.81[AMR][1000 genomes]
rs3776788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797494	0.86[ASN][1000 genomes]
rs3797497	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3797500	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357234	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52307000-52333800	Weak transcription	Gastric	stomach
2	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:52317600-52333600	Weak transcription	Colonic Mucosa	Colon
4	chr5:52318400-52331800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:52322200-52333200	Weak transcription	Fetal Stomach	stomach
6	chr5:52323200-52329000	Enhancers	NHLF	lung
7	chr5:52323600-52332600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:52324200-52334200	Weak transcription	Spleen	Spleen
9	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
10	chr5:52324600-52332400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr5:52325400-52329200	Enhancers	HUVEC	blood vessel
12	chr5:52326400-52329200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr5:52326400-52329400	Enhancers	Dnd41	blood
14	chr5:52326400-52329400	Enhancers	Hela-S3	cervix
15	chr5:52326600-52329200	Enhancers	NHDF-Ad	bronchial
16	chr5:52326800-52329000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:52326800-52329400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr5:52327000-52329000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr5:52327000-52329200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr5:52327200-52329200	Enhancers	HMEC	breast
21	chr5:52327400-52329200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr5:52327600-52329000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:52327600-52333000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:52327800-52329400	Enhancers	Osteobl	bone
25	chr5:52327800-52330400	Weak transcription	Fetal Kidney	kidney
26	chr5:52327800-52332200	Weak transcription	Esophagus	oesophagus
27	chr5:52327800-52333800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr5:52327800-52334400	Weak transcription	Pancreas	Pancrea
29	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:52328000-52332600	Weak transcription	Colon Smooth Muscle	Colon
31	chr5:52328000-52332800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:52328000-52333000	Weak transcription	HSMM	muscle
33	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
34	chr5:52328200-52329200	Enhancers	A549	lung
35	chr5:52328200-52332000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:52328400-52329200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:52328400-52330400	Weak transcription	Brain Substantia Nigra	brain
38	chr5:52328400-52332000	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:52328400-52333000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:52328400-52333000	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:52328400-52333800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:52328600-52329000	Enhancers	Lung	lung
43	chr5:52328600-52329200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:52328600-52329200	Enhancers	Small Intestine	intestine
45	chr5:52328600-52329200	Enhancers	Stomach Mucosa	stomach
46	chr5:52328600-52329400	Genic enhancers	NHEK	skin
47	chr5:52328600-52335200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr5:52328800-52329000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:52328800-52329000	Genic enhancers	HepG2	liver
50	chr5:52328800-52329200	Weak transcription	Brain Angular Gyrus	brain

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