Variant report

Variant	rs2431123
Chromosome Location	chr5:179307331-179307332
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:179306612-179307473	MCF-7	breast:	n/a	n/a
2	POLR2A	chr5:179307242-179307469	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179305601..179308758-chr5:179317802..179320775,3	MCF-7	breast:
2	chr5:179307319..179310872-chr5:179333429..179336113,3	MCF-7	breast:
3	chr5:179306460..179309457-chr5:179314767..179316995,2	MCF-7	breast:

Variant related genes	Relation type
TBC1D9B	TF binding region
ENSG00000197226	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs152233	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs152236	0.82[ASN][1000 genomes]
rs152237	0.82[ASN][1000 genomes]
rs152238	0.82[ASN][1000 genomes]
rs155791	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs155795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs155796	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs155797	0.84[ASN][1000 genomes]
rs156101	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs156104	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1684973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs182086	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs248217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs248218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs248220	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs248222	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs248232	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs248252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26074	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26075	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs26077	0.80[EUR][1000 genomes]
rs26078	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27411	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27471	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27474	0.80[ASN][1000 genomes]
rs28325	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30381	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30382	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30385	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs32437	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32461	0.85[CHB][hapmap];0.91[ASN][1000 genomes]
rs32469	0.88[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32470	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32471	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32472	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3734003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs43155	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs467764	0.81[JPT][hapmap]
rs532795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs574997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs578659	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs860706	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs88183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9957	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]

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	nsv883286	chr5:179290845-179313656	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2431123	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL
rs2431123	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	chr5:179286600-179310600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:179286600-179310800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr5:179286600-179311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:179287200-179333600	Weak transcription	Right Atrium	heart
6	chr5:179287800-179310000	Weak transcription	Fetal Brain Male	brain
7	chr5:179288400-179308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:179288400-179308400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:179289000-179308800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr5:179289000-179309200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:179289200-179307800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr5:179289200-179308600	Strong transcription	Liver	Liver
14	chr5:179289200-179308600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr5:179289200-179308800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:179289200-179309200	Strong transcription	Fetal Brain Female	brain
17	chr5:179289400-179307400	Strong transcription	Primary T cells from cord blood	blood
18	chr5:179289400-179307600	Strong transcription	Primary B cells from peripheral blood	blood
19	chr5:179289400-179308200	Strong transcription	Dnd41	blood
20	chr5:179289400-179308400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:179289400-179308400	Strong transcription	Ovary	ovary
22	chr5:179289400-179308400	Strong transcription	Stomach Smooth Muscle	stomach
23	chr5:179289400-179308400	Strong transcription	Thymus	Thymus
24	chr5:179289400-179309400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:179289600-179308800	Strong transcription	Brain Germinal Matrix	brain
26	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
27	chr5:179289800-179308400	Strong transcription	Lung	lung
28	chr5:179290200-179307800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:179290200-179308600	Strong transcription	Fetal Intestine Small	intestine
30	chr5:179290400-179308800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:179290400-179309600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:179291000-179308400	Strong transcription	Fetal Intestine Large	intestine
33	chr5:179291200-179308600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:179292800-179308400	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr5:179293400-179307600	Strong transcription	Brain Angular Gyrus	brain
36	chr5:179293600-179309000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr5:179293600-179309000	Strong transcription	Placenta	Placenta
38	chr5:179293800-179309400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr5:179294000-179308400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:179295000-179309200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr5:179295400-179308200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr5:179295400-179309000	Strong transcription	Duodenum Mucosa	Duodenum
44	chr5:179296000-179308400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:179296200-179308400	Strong transcription	A549	lung
46	chr5:179296400-179308000	Strong transcription	Brain Hippocampus Middle	brain
47	chr5:179296400-179308200	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr5:179296600-179308200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr5:179296800-179307600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr5:179296800-179309400	Weak transcription	HUVEC	blood vessel

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