Variant report

Variant	rs34857879
Chromosome Location	chr5:177046240-177046241
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	chr5:177036778..177039311-chr5:177043869..177047459,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B4GALT7-1	chr5:177045917-177046755	ENSG00000247679.2
2	lnc-B4GALT7-1	chr5:177045643-177046865	NONHSAT105444
3	lnc-B4GALT7-1	chr5:177045917-177047505	NONHSAT105447

Variant related genes	Relation type
ENSG00000247679	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12515264	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12515554	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13169820	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13175194	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13175367	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13185565	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13187467	0.85[EUR][1000 genomes]
rs28587776	0.82[EUR][1000 genomes]
rs34457379	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34582406	0.80[EUR][1000 genomes]
rs34708092	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36092039	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs461259	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62398479	0.82[EUR][1000 genomes]
rs72815179	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7718106	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916108	chr5:176688459-177078723	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
2	nsv1024444	chr5:176751921-177427715	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	142 gene(s)	inside rSNPs	diseases
3	esv2752795	chr5:176898619-177488281	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
4	nsv883182	chr5:176980995-177322056	Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs34857879	FAM153C	cis	Esophagus Muscularis	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177028400-177048400	Weak transcription	NH-A	brain
2	chr5:177028600-177046400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:177028600-177049000	Weak transcription	HUVEC	blood vessel
4	chr5:177028600-177053200	Weak transcription	HSMM	muscle
5	chr5:177029000-177054200	Weak transcription	Brain Substantia Nigra	brain
6	chr5:177034400-177048600	Weak transcription	A549	lung
7	chr5:177034800-177052200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:177035000-177046600	Weak transcription	Fetal Brain Male	brain
9	chr5:177035000-177051000	Weak transcription	Stomach Mucosa	stomach
10	chr5:177035000-177054200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:177035200-177053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:177036600-177048000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:177037000-177055200	Weak transcription	NHLF	lung
14	chr5:177037200-177047400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:177038600-177054400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:177039400-177051400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr5:177041600-177050200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr5:177041600-177054400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:177042800-177046600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:177043000-177048800	Strong transcription	Fetal Brain Female	brain
21	chr5:177043200-177047400	Strong transcription	Dnd41	blood
22	chr5:177043200-177048600	Strong transcription	Adipose Nuclei	Adipose
23	chr5:177043400-177047800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:177043400-177050000	Strong transcription	Ovary	ovary
25	chr5:177043400-177052800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr5:177043600-177046800	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:177043600-177051800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:177043800-177046600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:177043800-177046800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:177043800-177046800	Strong transcription	Brain Anterior Caudate	brain
31	chr5:177043800-177049800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr5:177044000-177047800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:177044000-177047800	Strong transcription	Primary B cells from cord blood	blood
34	chr5:177044000-177047800	Strong transcription	Primary T cells from cord blood	blood
35	chr5:177044000-177051400	Weak transcription	HMEC	breast
36	chr5:177044200-177046400	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:177044400-177046600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr5:177044400-177047800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr5:177044400-177048800	Strong transcription	Fetal Lung	lung
40	chr5:177044400-177049000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:177044400-177050000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:177044400-177061800	Weak transcription	Small Intestine	intestine
43	chr5:177044600-177046400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr5:177044600-177046400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:177044600-177046800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:177044600-177047000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:177044600-177047000	Strong transcription	Colon Smooth Muscle	Colon
48	chr5:177044600-177047200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr5:177044600-177047200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:177044600-177047400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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