Variant report

Variant	rs9957
Chromosome Location	chr5:179290154-179290155
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179289998-179290162	A549	lung:	n/a	n/a
2	POLR2A	chr5:179289838-179290236	K562	blood:	n/a	n/a
3	POLR2A	chr5:179289978-179290223	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:179288966..179290772-chr5:179295721..179297520,3	MCF-7	breast:
2	chr5:179290040..179292104-chr5:179300801..179303635,2	K562	blood:
3	chr5:179288672..179291374-chr5:179292378..179294390,2	MCF-7	breast:
4	chr5:179289788..179295879-chr5:179298486..179302200,7	MCF-7	breast:
5	chr5:179288312..179290452-chr5:179293485..179295109,2	MCF-7	breast:

No data

Variant related genes	Relation type
C5orf45	TF binding region
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs13164817	1.00[YRI][hapmap]
rs152233	0.85[ASN][1000 genomes]
rs155791	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs155795	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs155796	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs155797	0.80[ASN][1000 genomes]
rs156101	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs156104	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1684973	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs182086	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2431123	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2431124	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2434411	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248216	1.00[YRI][hapmap]
rs248217	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs248218	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248219	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs248220	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs248222	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs248252	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs26074	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap]
rs26075	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs26078	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs27410	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27411	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28325	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs30381	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30382	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30385	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30386	0.81[CHB][hapmap]
rs32437	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32438	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs32461	0.87[ASN][1000 genomes]
rs32469	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap]
rs32471	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs32472	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3734003	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs43155	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs469318	1.00[YRI][hapmap]
rs532795	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs574997	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs578659	0.82[AMR][1000 genomes]
rs860706	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs88183	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS 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	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
3	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
4	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
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	nsv823362	chr5:179289854-179290413	Strong transcription Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9957	TBC1D9B	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179286200-179310600	Weak transcription	Stomach Mucosa	stomach
2	chr5:179286400-179303000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:179286600-179290400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:179286600-179290800	Weak transcription	Primary B cells from cord blood	blood
5	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:179286800-179290400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:179287200-179290400	Weak transcription	HMEC	breast
10	chr5:179287200-179296400	Weak transcription	HUVEC	blood vessel
11	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
12	chr5:179287400-179294600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr5:179287600-179291000	Weak transcription	Colon Smooth Muscle	Colon
14	chr5:179287600-179291800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:179287800-179296800	Weak transcription	Fetal Heart	heart
16	chr5:179287800-179302200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:179287800-179310000	Weak transcription	Fetal Brain Male	brain
18	chr5:179288400-179290200	ZNF genes & repeats	Fetal Muscle Leg	muscle
19	chr5:179288400-179291200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:179288400-179292400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:179288400-179292400	Strong transcription	HSMM	muscle
22	chr5:179288400-179308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:179288400-179308400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:179288600-179290200	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr5:179288800-179290400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
27	chr5:179288800-179290800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr5:179288800-179291000	ZNF genes & repeats	Fetal Intestine Large	intestine
29	chr5:179288800-179292400	Strong transcription	A549	lung
30	chr5:179289000-179290200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
31	chr5:179289000-179290200	Strong transcription	K562	blood
32	chr5:179289000-179290400	ZNF genes & repeats	Placenta	Placenta
33	chr5:179289000-179292000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:179289000-179292000	Strong transcription	Brain Anterior Caudate	brain
35	chr5:179289000-179294200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr5:179289000-179294400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:179289000-179294600	Strong transcription	Fetal Lung	lung
38	chr5:179289000-179295200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr5:179289000-179295200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr5:179289000-179300400	Strong transcription	Osteobl	bone
41	chr5:179289000-179306800	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr5:179289000-179307000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr5:179289000-179308800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr5:179289000-179309200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr5:179289200-179290200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr5:179289200-179290200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
47	chr5:179289200-179290200	Strong transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:179289200-179290400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:179289200-179290400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:179289200-179290400	ZNF genes & repeats	Fetal Stomach	stomach

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