Variant report

Variant	rs152233
Chromosome Location	chr5:179332982-179332983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179231022..179234564-chr5:179332456..179334964,4	MCF-7	breast:
2	chr5:179231951..179234998-chr5:179332268..179335922,5	MCF-7	breast:
3	chr5:179312827..179319105-chr5:179330918..179335028,6	MCF-7	breast:
4	chr5:179247957..179250042-chr5:179330844..179333661,2	K562	blood:
5	chr5:179232711..179234875-chr5:179332233..179334161,2	K562	blood:
6	chr5:179325019..179329362-chr5:179330614..179334824,8	K562	blood:
7	chr5:179246876..179249284-chr5:179332914..179335716,2	MCF-7	breast:
8	chr5:179320962..179322826-chr5:179332050..179333678,2	K562	blood:
9	chr5:179284572..179287253-chr5:179332885..179335031,4	MCF-7	breast:
10	chr5:179332761..179336643-chr5:179497180..179500753,5	MCF-7	breast:
11	chr5:179297185..179299708-chr5:179331980..179334560,2	K562	blood:
12	chr5:179284802..179287636-chr5:179331072..179333036,2	MCF-7	breast:
13	chr5:179220191..179222591-chr5:179331659..179334767,3	MCF-7	breast:
14	chr5:179332164..179334090-chr5:179510604..179512176,2	MCF-7	breast:
15	chr5:179263833..179265352-chr5:179332066..179334694,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000161013	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161010	Chromatin interaction
ENSG00000113269	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000245317	Chromatin interaction
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs152232	0.80[EUR][1000 genomes]
rs152236	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs152237	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs152238	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs155791	0.85[ASN][1000 genomes]
rs155795	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs155796	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs155797	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs156101	0.84[EUR][1000 genomes]
rs156104	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1684973	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs182086	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2431123	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2431124	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2434411	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs248218	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248219	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs248222	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs248232	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs248252	0.90[ASN][1000 genomes]
rs26074	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26075	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26077	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26078	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27410	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27411	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs27471	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27474	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28325	0.88[ASN][1000 genomes]
rs30381	0.90[ASN][1000 genomes]
rs30382	0.90[ASN][1000 genomes]
rs30385	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32437	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32438	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32461	0.86[ASN][1000 genomes]
rs32469	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32470	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs32471	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs32472	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3734003	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs43155	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs532795	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs574997	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs860706	0.90[ASN][1000 genomes]
rs88183	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9957	0.85[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	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
3	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
4	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
6	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
7	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs152233	TBC1D9B	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
2	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:179311400-179333800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:179312000-179333000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:179312000-179333400	Weak transcription	Fetal Brain Male	brain
6	chr5:179312200-179333200	Strong transcription	Placenta	Placenta
7	chr5:179312800-179333400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179313000-179333000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:179313200-179333200	Strong transcription	Fetal Stomach	stomach
10	chr5:179313600-179333400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179313800-179333200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr5:179315400-179333200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:179320400-179333600	Weak transcription	Stomach Mucosa	stomach
14	chr5:179320800-179333200	Weak transcription	Small Intestine	intestine
15	chr5:179320800-179333400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr5:179321000-179333600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:179321200-179333200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:179324400-179333000	Strong transcription	NHEK	skin
19	chr5:179325000-179333400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:179326400-179333800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:179326600-179333400	Weak transcription	Fetal Heart	heart
22	chr5:179326800-179333400	Weak transcription	NH-A	brain
23	chr5:179326800-179333400	Weak transcription	NHDF-Ad	bronchial
24	chr5:179327000-179333600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr5:179328200-179333600	Weak transcription	Psoas Muscle	Psoas
26	chr5:179329000-179333000	Strong transcription	Esophagus	oesophagus
27	chr5:179329000-179333200	Strong transcription	A549	lung
28	chr5:179329400-179333000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:179329600-179333200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr5:179329600-179333600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:179329800-179333000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:179329800-179333000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:179329800-179333600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr5:179330000-179333200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:179330800-179333200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr5:179330800-179333400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:179331000-179333200	Weak transcription	Brain Substantia Nigra	brain
38	chr5:179331000-179333400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr5:179331000-179333600	Weak transcription	Fetal Kidney	kidney
40	chr5:179331200-179333200	Weak transcription	Colonic Mucosa	Colon
41	chr5:179331200-179333200	Weak transcription	GM12878-XiMat	blood
42	chr5:179331200-179333400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr5:179331200-179333400	Weak transcription	HSMMtube	muscle
44	chr5:179331400-179333400	Weak transcription	Primary T cells from cord blood	blood
45	chr5:179331600-179333200	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:179331600-179333400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr5:179331800-179333000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:179331800-179333200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:179331800-179333200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:179331800-179333200	Weak transcription	Fetal Thymus	thymus

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