Variant report

Variant	rs783422
Chromosome Location	chr6:106958870-106958871
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	KAP1	chr6:106958538-106958898	HEK293	kidney:	n/a	n/a
2	BCLAF1	chr6:106958311-106958873	GM12878	blood:	n/a	chr6:106958646-106958659
3	E2F4	chr6:106958493-106958887	GM12878	blood:	n/a	n/a
4	MTA3	chr6:106958449-106959016	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:106957807-106960924	MCF10A-Er-Src	breast:	n/a	n/a
6	MAX	chr6:106957760-106958927	NB4	blood:	n/a	chr6:106958601-106958611
7	USF2	chr6:106958796-106958879	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:106958055-106958997	PANC-1	pancreas:	n/a	n/a
9	MAX	chr6:106958119-106958960	A549	lung:	n/a	chr6:106958601-106958611
10	MAX	chr6:106958258-106958878	MCF-7	breast:	n/a	chr6:106958601-106958611
11	MXI1	chr6:106957694-106959152	SK-N-SH	brain:	n/a	n/a
12	CTBP2	chr6:106957957-106958900	H1-hESC	embryonic stem cell:	n/a	n/a
13	ZEB1	chr6:106958349-106958913	GM12878	blood:	n/a	n/a
14	MTA3	chr6:106958286-106958942	GM12878	blood:	n/a	n/a
15	MXI1	chr6:106958338-106958931	GM12878	blood:	n/a	n/a
16	MYC	chr6:106957904-106958977	MCF10A-Er-Src	breast:	n/a	chr6:106958601-106958611
17	STAT3	chr6:106958701-106958998	MCF10A-Er-Src	breast:	n/a	n/a
18	ZEB1	chr6:106958258-106959008	HepG2	liver:	n/a	n/a
19	MYC	chr6:106958510-106959102	MCF10A-Er-Src	breast:	n/a	chr6:106958601-106958611
20	POLR2A	chr6:106958379-106958938	MCF10A-Er-Src	breast:	n/a	n/a
21	RUNX3	chr6:106958273-106958873	GM12878	blood:	n/a	n/a
22	RCOR1	chr6:106958454-106958959	GM12878	blood:	n/a	n/a
23	E2F4	chr6:106957768-106959295	MCF10A-Er-Src	breast:	n/a	chr6:106958287-106958299
24	SIN3AK20	chr6:106958076-106958962	PANC-1	pancreas:	n/a	n/a
25	ELF1	chr6:106958117-106958897	GM12878	blood:	n/a	n/a
26	PML	chr6:106958294-106958915	GM12878	blood:	n/a	n/a
27	ZNF263	chr6:106958279-106958969	HEK293-T-REx	kidney:	n/a	chr6:106958846-106958855 chr6:106958689-106958698
28	MAX	chr6:106958413-106958955	MCF-7	breast:	n/a	chr6:106958601-106958611
29	FOS	chr6:106958659-106958949	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr6:106958712-106959006	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr6:106957852-106958993	Raji	blood:	n/a	n/a
32	SIN3AK20	chr6:106958337-106958882	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr6:106958092-106959982	H1-neurons	neurons:	n/a	n/a
34	STAT3	chr6:106958666-106958999	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr6:106957957-106958978	PANC-1	pancreas:	n/a	n/a
36	TCF7L2	chr6:106958316-106958988	PANC-1	pancreas:	n/a	n/a
37	MAX	chr6:106958272-106958893	HepG2	liver:	n/a	chr6:106958601-106958611
38	MAX	chr6:106958242-106958907	SK-N-SH	brain:	n/a	chr6:106958601-106958611
39	SIN3A	chr6:106958189-106958933	H1-hESC	embryonic stem cell:	n/a	chr6:106958644-106958655
40	NFYB	chr6:106958145-106958875	GM12878	blood:	n/a	chr6:106958245-106958260 chr6:106958245-106958260
41	POLR2A	chr6:106958215-106958874	GM15510	blood:	n/a	n/a
42	MAX	chr6:106958202-106958999	HepG2	liver:	n/a	chr6:106958601-106958611
43	POLR2A	chr6:106958326-106958961	U87	brain:	n/a	n/a
44	MAX	chr6:106958406-106958894	SK-N-SH	brain:	n/a	chr6:106958601-106958611
45	NFIC	chr6:106958327-106958877	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:106957864-106958968	HL-60	blood:	n/a	n/a
47	POLR2A	chr6:106957853-106959025	HL-60	blood:	n/a	n/a
48	STAT3	chr6:106958693-106958952	MCF10A-Er-Src	breast:	n/a	n/a
49	FOXM1	chr6:106958369-106958887	GM12878	blood:	n/a	n/a
50	FOS	chr6:106958690-106958892	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:106955204..106959628-chr6:106966256..106969365,4	K562	blood:
2	chr6:106957571..106959305-chr6:106960058..106962439,2	MCF-7	breast:
3	chr6:106956358..106959318-chr6:106991274..106994095,2	MCF-7	breast:

Variant related genes	Relation type
AIM1	TF binding region
ENSG00000112297	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs710096	1.00[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs710097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs783404	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783417	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs783420	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs783423	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs936497	0.88[CHB][hapmap]

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	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv1025510	chr6:106791080-106982400	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv538404	chr6:106791080-106982400	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs783422	EEF1A2	trans	lymphoblastoid	seeQTL
rs783422	PRDM1	cis	lymphoblastoid	seeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106956800-106959600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr6:106957000-106959200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
3	chr6:106957000-106962800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:106957200-106960000	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr6:106957200-106961200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr6:106957200-106961600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:106957200-106962800	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr6:106957400-106959000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:106957400-106959000	Flanking Active TSS	Thymus	Thymus
10	chr6:106957400-106959200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:106957400-106959400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
12	chr6:106957400-106959800	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
13	chr6:106957400-106960200	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr6:106957400-106962200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:106957400-106963400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
16	chr6:106957600-106959000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:106957600-106959000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
18	chr6:106957600-106959000	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:106957600-106959000	Flanking Bivalent TSS/Enh	NH-A	brain
20	chr6:106957600-106959600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
21	chr6:106957600-106959800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr6:106957600-106961000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
25	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
26	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
27	chr6:106957800-106959000	Flanking Bivalent TSS/Enh	Osteobl	bone
28	chr6:106957800-106959400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr6:106957800-106959600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:106957800-106959800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr6:106957800-106961400	Active TSS	Right Atrium	heart
32	chr6:106958000-106959000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
33	chr6:106958000-106959000	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
34	chr6:106958000-106959000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr6:106958000-106959000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
36	chr6:106958000-106959000	Active TSS	A549	lung
37	chr6:106958000-106959200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:106958000-106959200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:106958000-106959400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:106958000-106959400	Active TSS	Small Intestine	intestine
41	chr6:106958000-106959400	Active TSS	HSMM	muscle
42	chr6:106958000-106960000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
43	chr6:106958000-106961000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
44	chr6:106958200-106959200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:106958200-106959200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:106958200-106959600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:106958200-106959800	Bivalent Enhancer	Fetal Heart	heart
48	chr6:106958200-106961200	Active TSS	NHDF-Ad	bronchial
49	chr6:106958400-106959000	Flanking Active TSS	Liver	Liver
50	chr6:106958400-106959000	Active TSS	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links