Variant report

Variant	rs9468830
Chromosome Location	chr6:30749712-30749713
allele	G/T
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	HNF4G	chr6:30749507-30750029	HepG2	liver:	n/a	n/a
2	EP300	chr6:30749179-30750877	A549	lung:	n/a	chr6:30749928-30749942
3	USF1	chr6:30749424-30749958	A549	lung:	n/a	chr6:30749653-30749664
4	EBF1	chr6:30749624-30750069	GM12878	blood:	n/a	chr6:30749894-30749905
5	MAFK	chr6:30749282-30750413	K562	blood:	n/a	n/a
6	USF2	chr6:30749465-30749852	HepG2	liver:	n/a	n/a
7	RAD21	chr6:30749316-30750284	A549	lung:	n/a	n/a
8	NFATC1	chr6:30749523-30750101	GM12878	blood:	n/a	n/a
9	TEAD4	chr6:30749337-30750165	SK-N-SH	brain:	n/a	n/a
10	SPI1	chr6:30749697-30750132	GM12878	blood:	n/a	chr6:30749933-30749942 chr6:30749984-30749997
11	CEBPB	chr6:30749245-30750831	A549	lung:	n/a	chr6:30750630-30750641 chr6:30749779-30749790
12	POLR2A	chr6:30749646-30749981	GM12878	blood:	n/a	n/a
13	TCF12	chr6:30749069-30751165	A549	lung:	n/a	n/a
14	IKZF1	chr6:30749671-30750061	GM12878	blood:	n/a	n/a
15	ELF1	chr6:30749511-30750144	MCF-7	breast:	n/a	n/a
16	RCOR1	chr6:30749391-30750323	K562	blood:	n/a	n/a
17	GABPA	chr6:30749543-30750057	MCF-7	breast:	n/a	n/a
18	BCL3	chr6:30749287-30750863	A549	lung:	n/a	chr6:30749933-30749942
19	USF1	chr6:30749372-30749901	SK-N-SH_RA	brain:	n/a	chr6:30749653-30749664
20	GABPA	chr6:30749470-30750198	HL-60	blood:	n/a	n/a
21	GABPA	chr6:30749709-30749952	HepG2	liver:	n/a	n/a
22	TCF7L2	chr6:30749293-30750024	Hela-S3	cervix:	n/a	n/a
23	FOXM1	chr6:30749405-30750796	ECC-1	luminal epithelium:	n/a	n/a
24	ELF1	chr6:30749480-30750105	K562	blood:	n/a	n/a
25	MYC	chr6:30749448-30749955	MCF10A-Er-Src	breast:	n/a	n/a
26	FOXA1	chr6:30749497-30750920	HepG2	liver:	n/a	n/a
27	RCOR1	chr6:30749243-30750915	Hela-S3	cervix:	n/a	n/a
28	CEBPB	chr6:30749485-30750808	HepG2	liver:	n/a	chr6:30750630-30750641 chr6:30749779-30749790
29	SP1	chr6:30749163-30751008	A549	lung:	n/a	n/a
30	TBL1XR1	chr6:30749283-30750277	K562	blood:	n/a	n/a
31	SPI1	chr6:30749651-30750120	K562	blood:	n/a	chr6:30749933-30749942 chr6:30749984-30749997
32	FOXA2	chr6:30749601-30750791	HepG2	liver:	n/a	n/a
33	POLR2A	chr6:30749027-30751412	Hela-S3	cervix:	n/a	n/a
34	JUND	chr6:30749212-30750239	SK-N-SH	brain:	n/a	n/a
35	EP300	chr6:30749480-30750734	K562	blood:	n/a	chr6:30749928-30749942
36	REST	chr6:30749444-30750040	HepG2	liver:	n/a	chr6:30749623-30749636
37	ZMIZ1	chr6:30749416-30750146	K562	blood:	n/a	n/a
38	USF2	chr6:30749220-30749969	Hela-S3	cervix:	n/a	n/a
39	MAFK	chr6:30749212-30750166	IMR90	lung:	n/a	n/a
40	POLR2A	chr6:30748460-30750969	Hela-S3	cervix:	n/a	n/a
41	ELF1	chr6:30749547-30750092	MCF-7	breast:	n/a	n/a
42	GATA3	chr6:30749594-30750267	T-47D	breast:	n/a	chr6:30749943-30749950
43	TBP	chr6:30749296-30750884	Hela-S3	cervix:	n/a	n/a
44	NR3C1	chr6:30749504-30750011	A549	lung:	n/a	n/a
45	MYC	chr6:30749439-30750360	K562	blood:	n/a	n/a
46	TCF12	chr6:30749360-30750691	A549	lung:	n/a	n/a
47	ZBTB33	chr6:30749512-30750046	A549	lung:	n/a	n/a
48	MXI1	chr6:30749476-30750732	HepG2	liver:	n/a	n/a
49	EP300	chr6:30749147-30750727	SK-N-SH	brain:	n/a	chr6:30749928-30749942
50	YY1	chr6:30749481-30750081	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30583409..30587215-chr6:30748473..30750740,4	K562	blood:
2	chr6:30657201..30658778-chr6:30748296..30750541,2	K562	blood:
3	chr6:30748758..30751430-chr6:30850690..30852588,5	MCF-7	breast:
4	chr6:30613838..30616795-chr6:30748344..30751338,2	K562	blood:
5	chr6:30748393..30749996-chr6:30841265..30843895,2	K562	blood:
6	chr6:30747932..30749847-chr6:30861062..30862984,2	K562	blood:
7	chr6:30685130..30687169-chr6:30748703..30751412,3	K562	blood:
8	chr6:27100755..27102737-chr6:30749085..30751315,2	K562	blood:
9	chr6:30710424..30713995-chr6:30746295..30752430,9	K562	blood:

Variant related genes	Relation type
HCG20	TF binding region
ENSG00000237775	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000137331	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10947091	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10947095	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11758688	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526481	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12527415	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12527745	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13196596	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13197105	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13197117	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13197227	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13201769	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201901	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206009	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13207758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210146	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211218	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213720	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16897899	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16897900	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28780116	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28780119	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894083	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894084	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894085	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28894089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3131042	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131043	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131046	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3131051	0.93[ASN][1000 genomes]
rs4711228	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711229	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713360	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713362	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4713365	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713366	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713367	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713368	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900029	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920124	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740474	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7740525	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9295912	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9295914	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461630	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468832	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9468833	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
8	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
9	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
10	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv527226	chr6:30716719-30772378	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv884103	chr6:30729487-30755668	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
13	nsv884104	chr6:30740680-30753146	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9468830	NKAPL	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30744000-30758000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:30746000-30749800	Enhancers	Pancreas	Pancrea
3	chr6:30746000-30750000	Enhancers	Left Ventricle	heart
4	chr6:30746000-30750400	Enhancers	Fetal Stomach	stomach
5	chr6:30746000-30750400	Enhancers	Spleen	Spleen
6	chr6:30746000-30750800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:30746000-30750800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:30746000-30751000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:30746000-30752400	Enhancers	Placenta	Placenta
10	chr6:30746200-30751400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:30746600-30750400	Enhancers	Aorta	Aorta
12	chr6:30746600-30751000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr6:30746800-30751200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:30747000-30750600	Enhancers	HUVEC	blood vessel
15	chr6:30747000-30751400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:30747200-30751000	Enhancers	Right Ventricle	heart
17	chr6:30747400-30750600	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr6:30747400-30751000	Enhancers	NHLF	lung
19	chr6:30747600-30750000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:30747600-30750000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr6:30747600-30750000	Enhancers	HMEC	breast
22	chr6:30747800-30749800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr6:30748200-30750600	Enhancers	Primary hematopoietic stem cells	blood
24	chr6:30748200-30751400	Enhancers	Liver	Liver
25	chr6:30748200-30753800	Weak transcription	Primary T cells from cord blood	blood
26	chr6:30748600-30750000	Enhancers	Psoas Muscle	Psoas
27	chr6:30748600-30750800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr6:30748800-30749800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:30748800-30749800	Enhancers	Ovary	ovary
30	chr6:30748800-30750000	Flanking Active TSS	Stomach Smooth Muscle	stomach
31	chr6:30748800-30750200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:30748800-30751000	Enhancers	Primary B cells from cord blood	blood
33	chr6:30748800-30751400	Enhancers	Fetal Intestine Small	intestine
34	chr6:30748800-30751400	Flanking Active TSS	Hela-S3	cervix
35	chr6:30749000-30749800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr6:30749000-30750400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:30749000-30750400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr6:30749000-30750600	Enhancers	Fetal Thymus	thymus
39	chr6:30749000-30750800	Enhancers	Small Intestine	intestine
40	chr6:30749000-30751200	Flanking Active TSS	HepG2	liver
41	chr6:30749200-30749800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:30749200-30749800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:30749200-30749800	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr6:30749200-30749800	Flanking Active TSS	Brain Substantia Nigra	brain
45	chr6:30749200-30749800	Flanking Active TSS	Fetal Heart	heart
46	chr6:30749200-30749800	Flanking Active TSS	Right Atrium	heart
47	chr6:30749200-30749800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr6:30749200-30749800	Flanking Active TSS	A549	lung
49	chr6:30749200-30750000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr6:30749200-30750000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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