Variant report

Variant	rs2431124
Chromosome Location	chr5:179309843-179309844
allele	A/C
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	SETDB1	chr5:179309305-179310567	K562	blood:	n/a	n/a
2	POLR2A	chr5:179309470-179310038	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179308524..179311732-chr5:179312804..179315984,3	K562	blood:
2	chr5:179305874..179308839-chr5:179309473..179313731,6	MCF-7	breast:
3	chr5:179307319..179310872-chr5:179333429..179336113,3	MCF-7	breast:
4	chr5:179299709..179302436-chr5:179308085..179309910,2	MCF-7	breast:

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

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs152233	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152236	0.84[ASN][1000 genomes]
rs152237	0.84[ASN][1000 genomes]
rs152238	0.84[ASN][1000 genomes]
rs155791	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs155795	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155796	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs155797	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs156101	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs156104	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1684973	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182086	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2431123	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];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs248217	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs248218	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248219	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs248220	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs248222	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs248232	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs248252	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26074	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs26075	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs26077	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs26078	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27410	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs27411	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27471	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs27474	0.82[ASN][1000 genomes]
rs28325	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30381	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30382	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs30385	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32437	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32438	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32461	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs32469	0.88[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs32470	0.83[ASN][1000 genomes]
rs32471	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs32472	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3734003	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs43155	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs467764	0.80[JPT][hapmap]
rs532795	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs574997	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578659	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs860706	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs88183	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9957	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]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
rs2431124	TBC1D9B	cis	Muscle Skeletal	GTEx
rs2431124	SQSTM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr5:179288400-179310600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:179289600-179328000	Strong transcription	Adipose Nuclei	Adipose
9	chr5:179295200-179334000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr5:179300400-179310200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:179302200-179310600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:179302400-179310800	Weak transcription	Psoas Muscle	Psoas
13	chr5:179304600-179310600	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr5:179305200-179310600	Weak transcription	HSMMtube	muscle
15	chr5:179305800-179310600	Weak transcription	Hela-S3	cervix
16	chr5:179306800-179310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:179306800-179310800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr5:179306800-179311600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:179307000-179310600	Weak transcription	Brain Substantia Nigra	brain
20	chr5:179307000-179310600	Weak transcription	Left Ventricle	heart
21	chr5:179307400-179310400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr5:179307600-179310800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr5:179307600-179310800	Weak transcription	Aorta	Aorta
24	chr5:179307800-179310600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr5:179308000-179310600	Weak transcription	Colonic Mucosa	Colon
26	chr5:179308200-179310200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:179308200-179310600	Weak transcription	NHLF	lung
28	chr5:179308400-179310000	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:179308400-179310800	Weak transcription	Right Ventricle	heart
30	chr5:179308400-179318600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:179308600-179310800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr5:179309200-179310200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr5:179309200-179310800	ZNF genes & repeats	Primary T cells from cord blood	blood
34	chr5:179309200-179311400	ZNF genes & repeats	Fetal Thymus	thymus
35	chr5:179309200-179311600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
36	chr5:179309200-179311600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
37	chr5:179309200-179311600	ZNF genes & repeats	Brain Germinal Matrix	brain
38	chr5:179309200-179311800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
39	chr5:179309200-179311800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:179309200-179312000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
41	chr5:179309200-179312000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr5:179309200-179312000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:179309200-179312000	ZNF genes & repeats	Fetal Brain Female	brain
44	chr5:179309200-179312200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr5:179309200-179312200	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr5:179309200-179312400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
47	chr5:179309200-179312400	ZNF genes & repeats	Fetal Lung	lung
48	chr5:179309200-179312800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:179309200-179312800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:179309200-179313600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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