Variant report

Variant	rs12520417
Chromosome Location	chr5:70847057-70847058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10942466	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10942683	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12110291	0.86[EUR][1000 genomes]
rs13158264	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13185743	0.85[EUR][1000 genomes]
rs1423358	0.84[EUR][1000 genomes]
rs149114	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs156754	0.80[ASN][1000 genomes]
rs156755	0.80[ASN][1000 genomes]
rs157044	0.87[AMR][1000 genomes]
rs157045	0.80[ASN][1000 genomes]
rs1698063	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs182190	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1833856	0.80[ASN][1000 genomes]
rs185733	0.80[ASN][1000 genomes]
rs190692	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2059193	0.85[EUR][1000 genomes]
rs2646639	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs276590	0.80[ASN][1000 genomes]
rs276591	0.80[ASN][1000 genomes]
rs276592	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs276593	0.80[ASN][1000 genomes]
rs276594	0.80[ASN][1000 genomes]
rs276595	0.80[ASN][1000 genomes]
rs276597	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs276598	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276599	0.81[ASN][1000 genomes]
rs276600	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs276601	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs277939	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277940	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs277944	0.80[ASN][1000 genomes]
rs277945	0.80[ASN][1000 genomes]
rs277966	0.80[AMR][1000 genomes]
rs279290	0.83[ASN][1000 genomes]
rs279291	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs279322	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34029702	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35327154	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36036841	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3761965	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs384732	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3890749	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs392791	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs404692	0.80[ASN][1000 genomes]
rs410776	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs418738	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs445771	0.80[ASN][1000 genomes]
rs451229	0.82[AMR][1000 genomes]
rs457908	0.80[ASN][1000 genomes]
rs458150	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs458534	0.84[ASN][1000 genomes]
rs459298	0.80[ASN][1000 genomes]
rs459787	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs460778	0.84[AMR][1000 genomes]
rs461215	0.80[ASN][1000 genomes]
rs462282	0.80[ASN][1000 genomes]
rs463871	0.80[ASN][1000 genomes]
rs466930	0.80[ASN][1000 genomes]
rs467160	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs467563	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467620	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs467851	0.80[ASN][1000 genomes]
rs467901	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs468028	0.80[ASN][1000 genomes]
rs468033	0.80[ASN][1000 genomes]
rs468128	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs468158	0.80[ASN][1000 genomes]
rs468446	0.80[ASN][1000 genomes]
rs468467	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs468564	0.80[ASN][1000 genomes]
rs468633	0.80[ASN][1000 genomes]
rs468658	0.80[ASN][1000 genomes]
rs468776	0.80[ASN][1000 genomes]
rs468832	0.80[ASN][1000 genomes]
rs469039	0.80[ASN][1000 genomes]
rs469369	0.80[ASN][1000 genomes]
rs469548	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs469617	0.80[ASN][1000 genomes]
rs541035	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62361813	0.87[AMR][1000 genomes]
rs7443763	0.85[EUR][1000 genomes]
rs7444320	0.83[ASN][1000 genomes]
rs7447545	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7732361	0.84[EUR][1000 genomes]
rs9791120	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs986217	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv882177	chr5:70800538-70856378	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv882178	chr5:70806958-70856378	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv882179	chr5:70807073-70856378	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
8	esv3422044	chr5:70846621-70849169	Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12520417	BDP1	Cis_1M	lymphoblastoid	RTeQTL
rs12520417	RP11-195E2.1	cis	Nerve Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70778400-70869600	Weak transcription	Stomach Mucosa	stomach
2	chr5:70820200-70857400	Weak transcription	Small Intestine	intestine
3	chr5:70822000-70847200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:70822600-70847400	Strong transcription	Dnd41	blood
5	chr5:70823200-70847200	Strong transcription	Primary T cells from cord blood	blood
6	chr5:70825200-70859600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:70825800-70869200	Weak transcription	Fetal Heart	heart
8	chr5:70827600-70847400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:70827600-70847400	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:70827600-70864400	Strong transcription	Liver	Liver
11	chr5:70827800-70847400	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:70828000-70847200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:70828000-70847600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:70829400-70847600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr5:70830600-70847800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr5:70831000-70847200	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr5:70831400-70847200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr5:70831400-70864600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:70833400-70847200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:70833800-70847600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:70833800-70847800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:70834000-70871800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:70834200-70862800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:70834400-70847400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr5:70834800-70847200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr5:70835000-70847400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:70835200-70847200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr5:70835200-70847400	Strong transcription	Fetal Intestine Large	intestine
29	chr5:70835600-70847200	Strong transcription	Fetal Lung	lung
30	chr5:70835800-70847600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr5:70835800-70850400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:70836400-70847600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:70836800-70847200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr5:70837000-70847400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:70837000-70848000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:70837200-70847400	Strong transcription	Stomach Smooth Muscle	stomach
37	chr5:70837400-70847200	Strong transcription	Primary B cells from cord blood	blood
38	chr5:70837400-70847400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:70837800-70847400	Strong transcription	Fetal Thymus	thymus
40	chr5:70837800-70861800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:70838000-70859400	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr5:70838200-70847200	Strong transcription	Fetal Muscle Leg	muscle
43	chr5:70838400-70847600	Strong transcription	Fetal Intestine Small	intestine
44	chr5:70838400-70847800	Strong transcription	Fetal Stomach	stomach
45	chr5:70838400-70850200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:70838800-70847400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr5:70838800-70847600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr5:70839200-70847400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:70839400-70870000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:70840400-70849800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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