Variant report

Variant	rs56007806
Chromosome Location	chr5:37664759-37664760
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	chr5:37664491..37667181-chr5:37703176..37705396,2	MCF-7	breast:
2	chr5:37662824..37665076-chr5:37668148..37670201,3	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10805627	0.95[ASN][1000 genomes]
rs10941358	0.96[ASN][1000 genomes]
rs10941359	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11739400	0.97[ASN][1000 genomes]
rs11740897	0.99[ASN][1000 genomes]
rs11742904	0.95[ASN][1000 genomes]
rs11745980	0.97[ASN][1000 genomes]
rs11747548	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11747900	0.99[ASN][1000 genomes]
rs11749563	0.85[ASN][1000 genomes]
rs11750837	0.94[ASN][1000 genomes]
rs11750840	0.94[ASN][1000 genomes]
rs12189078	0.89[ASN][1000 genomes]
rs12332088	0.99[ASN][1000 genomes]
rs12516955	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12520944	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12521063	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1356433	0.96[ASN][1000 genomes]
rs1400854	0.97[ASN][1000 genomes]
rs1517786	1.00[ASN][1000 genomes]
rs1589116	0.84[AFR][1000 genomes]
rs1589119	0.95[ASN][1000 genomes]
rs1996427	0.99[ASN][1000 genomes]
rs2176479	0.95[ASN][1000 genomes]
rs4242251	0.87[ASN][1000 genomes]
rs4257799	0.86[ASN][1000 genomes]
rs4343860	0.95[ASN][1000 genomes]
rs4371784	0.94[ASN][1000 genomes]
rs4451075	0.89[ASN][1000 genomes]
rs4482927	0.95[ASN][1000 genomes]
rs4516881	0.95[ASN][1000 genomes]
rs4516882	0.94[ASN][1000 genomes]
rs4541680	0.94[ASN][1000 genomes]
rs4582305	0.85[ASN][1000 genomes]
rs4594879	0.89[ASN][1000 genomes]
rs4608942	0.94[ASN][1000 genomes]
rs4618454	0.92[ASN][1000 genomes]
rs4869538	0.84[AFR][1000 genomes]
rs4869541	0.97[ASN][1000 genomes]
rs4869543	0.92[ASN][1000 genomes]
rs55708822	0.94[ASN][1000 genomes]
rs55732996	0.97[ASN][1000 genomes]
rs55742744	0.97[ASN][1000 genomes]
rs55849485	0.86[ASN][1000 genomes]
rs56051431	0.94[ASN][1000 genomes]
rs56051756	0.94[ASN][1000 genomes]
rs56100322	0.97[ASN][1000 genomes]
rs56412589	0.96[ASN][1000 genomes]
rs56832651	0.99[ASN][1000 genomes]
rs59378089	0.92[ASN][1000 genomes]
rs59409868	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59829323	0.94[ASN][1000 genomes]
rs60589722	0.96[ASN][1000 genomes]
rs61492379	0.89[ASN][1000 genomes]
rs62360907	0.90[ASN][1000 genomes]
rs62360910	0.94[ASN][1000 genomes]
rs6451329	0.96[ASN][1000 genomes]
rs6451330	0.96[ASN][1000 genomes]
rs6451331	0.96[ASN][1000 genomes]
rs6451333	1.00[ASN][1000 genomes]
rs6451337	0.94[ASN][1000 genomes]
rs6451339	0.93[ASN][1000 genomes]
rs6863936	0.99[ASN][1000 genomes]
rs6864924	0.88[ASN][1000 genomes]
rs6868428	1.00[ASN][1000 genomes]
rs6884551	0.94[ASN][1000 genomes]
rs6884569	0.94[ASN][1000 genomes]
rs6885057	0.99[ASN][1000 genomes]
rs6885329	0.96[ASN][1000 genomes]
rs6887215	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6887613	1.00[ASN][1000 genomes]
rs72743184	0.87[ASN][1000 genomes]
rs7702644	0.95[ASN][1000 genomes]
rs7703775	0.85[ASN][1000 genomes]
rs7725465	0.86[AMR][1000 genomes];0.97[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	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1015983	chr5:37240827-37666601	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv1034094	chr5:37406859-37666704	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv537731	chr5:37406859-37666704	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv880890	chr5:37443079-37681646	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56007806	LOC646719	cis	brain	BrainEAC

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37647000-37665400	Weak transcription	Primary B cells from cord blood	blood
2	chr5:37648000-37666000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:37654600-37671800	Weak transcription	Primary T cells from cord blood	blood
4	chr5:37656600-37671600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:37658600-37666000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:37658800-37665400	Weak transcription	Right Ventricle	heart
7	chr5:37658800-37665600	Weak transcription	Left Ventricle	heart
8	chr5:37658800-37667400	Weak transcription	Hela-S3	cervix
9	chr5:37659000-37668000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr5:37659000-37668000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:37659000-37668600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:37659400-37665400	Weak transcription	Brain Angular Gyrus	brain
13	chr5:37659800-37665400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:37661600-37665400	Weak transcription	Brain Substantia Nigra	brain
15	chr5:37661600-37665600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr5:37661800-37665000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:37662000-37665000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:37662000-37665400	Weak transcription	Brain Anterior Caudate	brain
19	chr5:37662000-37665400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr5:37662200-37665400	Weak transcription	Brain Hippocampus Middle	brain
21	chr5:37662200-37665400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr5:37662200-37665400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:37662600-37668200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr5:37662800-37667200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:37662800-37671800	Weak transcription	Small Intestine	intestine
26	chr5:37663000-37667600	Weak transcription	HepG2	liver
27	chr5:37663400-37666400	Weak transcription	A549	lung
28	chr5:37663600-37665200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:37663800-37665400	Weak transcription	HSMM	muscle
30	chr5:37664000-37664800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:37664000-37665400	Weak transcription	Fetal Lung	lung
32	chr5:37664000-37665400	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:37664000-37665400	Weak transcription	Fetal Stomach	stomach
34	chr5:37664000-37665400	Weak transcription	Ovary	ovary
35	chr5:37664000-37665400	Weak transcription	Pancreas	Pancrea
36	chr5:37664000-37665400	Weak transcription	Spleen	Spleen
37	chr5:37664000-37665400	Weak transcription	HSMMtube	muscle
38	chr5:37664000-37665600	Weak transcription	NHDF-Ad	bronchial
39	chr5:37664000-37665800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:37664000-37666000	Weak transcription	Fetal Intestine Large	intestine
41	chr5:37664000-37666000	Weak transcription	Lung	lung
42	chr5:37664000-37667800	Weak transcription	Fetal Intestine Small	intestine
43	chr5:37664000-37668600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr5:37664000-37668600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:37664000-37671800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:37664200-37665200	Weak transcription	Colon Smooth Muscle	Colon
47	chr5:37664200-37665200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr5:37664200-37665800	Weak transcription	Adipose Nuclei	Adipose
49	chr5:37664400-37667400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:37664400-37667400	Weak transcription	Osteobl	bone

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