Variant report

Variant	rs6838153
Chromosome Location	chr4:122720999-122721000
allele	A/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	JUN	chr4:122720661-122723088	K562	blood:	n/a	chr4:122722469-122722482
2	CEBPB	chr4:122720682-122721054	HepG2	liver:	n/a	n/a
3	HNF4G	chr4:122720583-122721037	HepG2	liver:	n/a	chr4:122720792-122720807
4	ZNF384	chr4:122720798-122721233	K562	blood:	n/a	n/a
5	MYC	chr4:122720980-122721273	K562	blood:	n/a	n/a
6	FOXA1	chr4:122720671-122721081	HepG2	liver:	n/a	n/a
7	HNF4G	chr4:122720603-122721015	HepG2	liver:	n/a	chr4:122720792-122720807
8	EP300	chr4:122720597-122721067	HepG2	liver:	n/a	n/a
9	TBL1XR1	chr4:122720800-122721118	K562	blood:	n/a	n/a
10	TBP	chr4:122720519-122721158	HepG2	liver:	n/a	n/a
11	FOXA1	chr4:122720529-122721050	HepG2	liver:	n/a	n/a
12	HNF4A	chr4:122720578-122721040	HepG2	liver:	n/a	chr4:122720793-122720808
13	POLR2A	chr4:122720715-122721313	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
2	chr4:122720772..122725008-chr4:122725244..122729002,8	K562	blood:
3	chr4:122616868..122619074-chr4:122720747..122723892,4	MCF-7	breast:

Variant related genes	Relation type
EXOSC9	TF binding region
ENSG00000123737	Chromatin interaction
ENSG00000145386	Chromatin interaction
ENSG00000164111	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11098645	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098646	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098648	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731917	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12502635	0.88[CHB][hapmap]
rs12512876	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12650359	0.88[CHB][hapmap]
rs1396080	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1507994	0.83[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507995	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17452156	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063165	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2071486	0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2221628	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3217753	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217771	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217773	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3217780	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828485	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3924987	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4077102	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4516739	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56077950	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56159666	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56311153	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58649165	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61217486	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534323	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67772833	0.92[EUR][1000 genomes]
rs6813653	0.81[ASN][1000 genomes]
rs6815790	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6821305	0.90[ASN][1000 genomes]
rs6823818	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6824258	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs6826506	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855269	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72680779	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7660548	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686084	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686200	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691955	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs769238	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs769246	0.88[EUR][1000 genomes]
rs7699776	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684587	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv461635	chr4:122633535-122720999	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv595357	chr4:122633535-122720999	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6838153	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL
rs6838153	BBS7	cis	cerebellum	SCAN
rs6838153	EXOSC9	cis	lymphoblastoid	seeQTL
rs6838153	BBS7	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122711800-122721800	Weak transcription	Fetal Stomach	stomach
2	chr4:122711800-122721800	Weak transcription	HMEC	breast
3	chr4:122712200-122721600	Weak transcription	A549	lung
4	chr4:122713200-122721000	Weak transcription	HSMMtube	muscle
5	chr4:122714600-122721800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:122715600-122721800	Enhancers	Fetal Thymus	thymus
7	chr4:122716200-122721000	Weak transcription	Fetal Heart	heart
8	chr4:122716200-122721800	Weak transcription	Osteobl	bone
9	chr4:122716800-122721600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:122717000-122721800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:122717400-122721800	Weak transcription	NHEK	skin
12	chr4:122717600-122721600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:122717600-122721800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr4:122717600-122721800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:122717600-122721800	Weak transcription	Fetal Lung	lung
16	chr4:122717600-122721800	Weak transcription	NH-A	brain
17	chr4:122717600-122721800	Weak transcription	NHLF	lung
18	chr4:122717600-122722000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:122717800-122721600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:122717800-122721800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:122717800-122721800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:122717800-122721800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr4:122717800-122721800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:122717800-122721800	Weak transcription	HUVEC	blood vessel
25	chr4:122718000-122721800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr4:122718000-122721800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:122718200-122721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr4:122718200-122721800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:122718200-122721800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:122718200-122721800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:122718200-122721800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr4:122718200-122721800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr4:122719400-122721200	Enhancers	Thymus	Thymus
34	chr4:122719400-122721600	Enhancers	Dnd41	blood
35	chr4:122720000-122721600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr4:122720200-122721000	Weak transcription	Fetal Intestine Small	intestine
37	chr4:122720200-122721200	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr4:122720200-122721400	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr4:122720400-122721000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr4:122720400-122721200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:122720400-122721200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr4:122720400-122721200	Enhancers	Liver	Liver
43	chr4:122720400-122721200	Enhancers	Brain Hippocampus Middle	brain
44	chr4:122720400-122721400	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr4:122720400-122721400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr4:122720400-122721600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr4:122720400-122721600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr4:122720400-122721800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr4:122720400-122722000	Flanking Active TSS	HepG2	liver
50	chr4:122720400-122722200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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