Variant report

Variant	rs9357232
Chromosome Location	chr6:36928459-36928460
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	GATA2	chr6:36928313-36928738	K562	blood:	n/a	chr6:36928483-36928492 chr6:36928463-36928472 chr6:36928464-36928481
2	NR2F2	chr6:36928307-36928760	K562	blood:	n/a	n/a
3	EGR1	chr6:36928295-36928675	K562	blood:	n/a	n/a
4	POLR2A	chr6:36928318-36928673	K562	blood:	n/a	n/a
5	MAFK	chr6:36928438-36928836	K562	blood:	n/a	n/a
6	EP300	chr6:36928319-36928741	K562	blood:	n/a	chr6:36928478-36928491
7	MYC	chr6:36928426-36928660	K562	blood:	n/a	n/a
8	GATA2	chr6:36928268-36928770	K562	blood:	n/a	chr6:36928483-36928492 chr6:36928463-36928472 chr6:36928464-36928481
9	GATA3	chr6:36928156-36928832	SK-N-SH	brain:	n/a	chr6:36928483-36928492 chr6:36928463-36928472 chr6:36928464-36928481
10	FOSL2	chr6:36928214-36928724	SK-N-SH	brain:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494
11	RCOR1	chr6:36928318-36928756	K562	blood:	n/a	n/a
12	MYC	chr6:36928302-36928695	K562	blood:	n/a	n/a
13	ETS1	chr6:36928428-36928690	K562	blood:	n/a	n/a
14	MAZ	chr6:36928041-36928722	K562	blood:	n/a	n/a
15	TAL1	chr6:36927956-36928783	K562	blood:	n/a	chr6:36928463-36928481
16	REST	chr6:36928352-36928576	K562	blood:	n/a	chr6:36928559-36928567
17	MYC	chr6:36928223-36928710	K562	blood:	n/a	n/a
18	JUND	chr6:36928444-36928559	HepG2	liver:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494
19	JUN	chr6:36928277-36928749	K562	blood:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494
20	UBTF	chr6:36928390-36928757	K562	blood:	n/a	n/a
21	TEAD4	chr6:36928141-36928868	K562	blood:	n/a	n/a
22	MAFF	chr6:36928443-36928673	K562	blood:	n/a	n/a
23	SMC3	chr6:36928360-36928719	Hela-S3	cervix:	n/a	n/a
24	HDAC2	chr6:36928267-36928770	K562	blood:	n/a	n/a
25	MAX	chr6:36928395-36928700	Hela-S3	cervix:	n/a	n/a
26	TBL1XR1	chr6:36928167-36928653	K562	blood:	n/a	n/a
27	JUN	chr6:36928300-36928737	K562	blood:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494
28	FOSL1	chr6:36928230-36928763	K562	blood:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494 chr6:36928483-36928494
29	GABPA	chr6:36928409-36928715	K562	blood:	n/a	n/a
30	MAZ	chr6:36928286-36928767	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr6:36928376-36928641	K562	blood:	n/a	n/a
32	BHLHE40	chr6:36928341-36928752	K562	blood:	n/a	n/a
33	GATA2	chr6:36928390-36928700	HUVEC	blood vessel:	n/a	chr6:36928483-36928492 chr6:36928463-36928472 chr6:36928464-36928481
34	EGR1	chr6:36928310-36928667	K562	blood:	n/a	n/a
35	CEBPD	chr6:36927892-36928849	K562	blood:	n/a	n/a
36	POLR2A	chr6:36928421-36928716	HCT-116	colon:	n/a	n/a
37	JUND	chr6:36928395-36928794	SK-N-SH	brain:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494
38	TEAD4	chr6:36928261-36928786	K562	blood:	n/a	n/a
39	HDAC2	chr6:36928404-36928715	K562	blood:	n/a	n/a
40	RAD21	chr6:36928424-36928652	K562	blood:	n/a	n/a
41	JUND	chr6:36928287-36928806	K562	blood:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494
42	POLR2A	chr6:36928388-36928720	K562	blood:	n/a	n/a
43	REST	chr6:36928311-36928619	K562	blood:	n/a	chr6:36928559-36928567
44	GATA3	chr6:36928279-36928768	SK-N-SH	brain:	n/a	chr6:36928483-36928492 chr6:36928463-36928472 chr6:36928464-36928481
45	POLR2A	chr6:36928398-36928807	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr6:36928419-36928701	HCT-116	colon:	n/a	n/a
47	GABPA	chr6:36928280-36928681	K562	blood:	n/a	n/a
48	ATF3	chr6:36928406-36928624	K562	blood:	n/a	n/a
49	CHD2	chr6:36928366-36928706	Hela-S3	cervix:	n/a	n/a
50	FOSL2	chr6:36928414-36928614	HepG2	liver:	n/a	chr6:36928483-36928495 chr6:36928485-36928493 chr6:36928484-36928494 chr6:36928484-36928494

No.	Distal block	Cell Line	Cell type
1	chr6:36927877..36929590-chr6:36935143..36936751,2	MCF-7	breast:
2	chr6:36920733..36923639-chr6:36925448..36929945,7	K562	blood:
3	chr6:36926514..36929766-chr6:36952495..36955671,4	MCF-7	breast:
4	chr6:36562786..36564332-chr6:36928250..36929910,2	K562	blood:
5	chr6:36921774..36924130-chr6:36928401..36929929,2	MCF-7	breast:
6	chr6:36925903..36928788-chr6:36946034..36948612,2	MCF-7	breast:
7	chr6:36926516..36929397-chr6:36985217..36986948,2	K562	blood:
8	chr6:36852067..36855564-chr6:36924677..36929209,4	K562	blood:

Variant related genes	Relation type
PI16	TF binding region
ENSG00000198663	Chromatin interaction
ENSG00000164530	Chromatin interaction
ENSG00000137409	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1023037	0.89[ASN][1000 genomes]
rs12191672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199301	1.00[JPT][hapmap]
rs17624546	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17624895	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2177845	0.89[ASN][1000 genomes]
rs2293388	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2293389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs3778022	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[EUR][1000 genomes]
rs3778024	0.82[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3778026	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3798477	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3798478	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4585544	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901560	0.84[GIH][hapmap];0.83[MEX][hapmap]
rs726819	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs734905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753634	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753635	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755143	0.96[GIH][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9380628	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv916833	chr6:36826524-37029833	Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv885815	chr6:36915906-36979583	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9357232	PI16	cis	parietal	SCAN
rs9357232	LPAR6	trans	lymphoblastoid	seeQTL
rs9357232	PI16	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36917600-36931200	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:36921800-36931200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr6:36922000-36931000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:36922200-36929200	Weak transcription	Spleen	Spleen
5	chr6:36923400-36930600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr6:36923400-36930600	Weak transcription	GM12878-XiMat	blood
7	chr6:36923400-36931000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:36923400-36931000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:36924000-36929000	Weak transcription	Esophagus	oesophagus
10	chr6:36924200-36928800	Weak transcription	Brain Anterior Caudate	brain
11	chr6:36924400-36929000	Weak transcription	Right Ventricle	heart
12	chr6:36924400-36929200	Weak transcription	Right Atrium	heart
13	chr6:36924600-36928600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:36924600-36930000	Weak transcription	Primary B cells from cord blood	blood
15	chr6:36924800-36930600	Weak transcription	Primary T cells from cord blood	blood
16	chr6:36926200-36928600	Weak transcription	Pancreas	Pancrea
17	chr6:36927000-36929400	Enhancers	K562	blood
18	chr6:36927000-36931600	Weak transcription	Lung	lung
19	chr6:36927200-36929200	Weak transcription	Gastric	stomach
20	chr6:36927200-36930400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:36927200-36930400	Enhancers	Fetal Thymus	thymus
22	chr6:36927200-36931000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:36927200-36931600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:36927200-36933400	Enhancers	Stomach Mucosa	stomach
25	chr6:36927400-36928600	Weak transcription	Left Ventricle	heart
26	chr6:36927400-36929200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:36927400-36929400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr6:36927400-36931000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:36927600-36928600	Enhancers	Hela-S3	cervix
30	chr6:36927600-36929200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:36927800-36928600	Enhancers	HSMMtube	muscle
32	chr6:36927800-36929000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
33	chr6:36927800-36929000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:36927800-36929000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:36927800-36929000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:36927800-36929000	Enhancers	Osteobl	bone
37	chr6:36927800-36929200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:36927800-36929200	Enhancers	NH-A	brain
39	chr6:36927800-36929200	Enhancers	NHEK	skin
40	chr6:36927800-36929400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:36927800-36929400	Enhancers	Duodenum Mucosa	Duodenum
42	chr6:36927800-36929800	Enhancers	Fetal Heart	heart
43	chr6:36927800-36933200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:36928000-36928800	Enhancers	HUVEC	blood vessel
45	chr6:36928000-36929000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr6:36928000-36929000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr6:36928000-36929000	Enhancers	A549	lung
48	chr6:36928000-36929400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:36928000-36929600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:36928000-36931200	Weak transcription	Stomach Smooth Muscle	stomach

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