Variant report

Variant	rs9262146
Chromosome Location	chr6:30656828-30656829
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30652434-30659300	HUVEC	blood vessel:	n/a	n/a
2	MXI1	chr6:30656401-30657039	GM12878	blood:	n/a	n/a
3	MTA3	chr6:30652443-30657175	GM12878	blood:	n/a	n/a
4	CTCF	chr6:30656740-30656890	GM12871	blood:	n/a	n/a
5	POLR2A	chr6:30653392-30659188	GM12892	blood:	n/a	n/a
6	POLR2A	chr6:30649497-30657006	HUVEC	blood vessel:	n/a	n/a
7	STAT5A	chr6:30656609-30657081	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:30653520-30657649	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr6:30656309-30657512	K562	blood:	n/a	n/a
10	POLR2A	chr6:30656437-30656864	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:30656278-30657141	GM12878	blood:	n/a	n/a
12	WRNIP1	chr6:30655733-30657165	GM12878	blood:	n/a	n/a
13	POLR2A	chr6:30656827-30656855	GM12878	blood:	n/a	n/a
14	PML	chr6:30653377-30656835	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:30649396-30659159	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:30653477-30656921	GM18526	blood:	n/a	n/a
17	MTA3	chr6:30656653-30657136	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:30653755-30659113	GM12878	blood:	n/a	n/a
19	POLR2A	chr6:30653800-30658021	GM19099	blood:	n/a	n/a
20	MAX	chr6:30656444-30656894	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:30653030-30656860	U87	brain:	n/a	n/a
22	POLR2A	chr6:30656370-30656863	GM19193	blood:	n/a	n/a
23	POLR2A	chr6:30656373-30657365	Raji	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30652587..30660257-chr6:30673612..30681352,12	MCF-7	breast:
2	chr6:30651552..30657864-chr6:30708721..30713716,15	MCF-7	breast:
3	chr6:30521801..30526749-chr6:30651868..30656911,6	K562	blood:
4	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
5	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
6	chr6:30580498..30587281-chr6:30649167..30662031,51	K562	blood:
7	chr6:30655802..30657936-chr6:30780184..30782576,2	K562	blood:
8	chr6:30586081..30587970-chr6:30654610..30657338,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPP1R18	TF binding region
ENSG00000196230	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000272540	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000137331	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000137337	Chromatin interaction
ENSG00000137312	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1059612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1264347	0.90[AMR][1000 genomes]
rs1264351	1.00[AMR][1000 genomes]
rs1264373	1.00[AMR][1000 genomes]
rs2263298	0.90[AMR][1000 genomes]
rs2517578	0.90[AMR][1000 genomes]
rs2524266	0.83[AMR][1000 genomes]
rs2535328	0.90[AMR][1000 genomes]
rs2535332	0.90[AMR][1000 genomes]
rs2535334	0.90[AMR][1000 genomes]
rs3094023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3094024	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3094118	0.80[EUR][1000 genomes]
rs3094125	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3095326	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3095327	0.85[EUR][1000 genomes]
rs3095328	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3095332	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129972	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3129973	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3129974	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3129984	0.91[AMR][1000 genomes]
rs3130117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130241	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3130658	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130660	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130665	0.80[EUR][1000 genomes]
rs3130668	0.91[AMR][1000 genomes]
rs3130670	0.83[AMR][1000 genomes]
rs3131112	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3132577	0.90[AMR][1000 genomes]
rs3132582	0.85[EUR][1000 genomes]
rs3132583	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132585	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3132610	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9262126	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262132	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262135	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9262141	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9262143	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv884086	chr6:30462084-30672757	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	798 gene(s)	inside rSNPs	diseases
6	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
7	nsv884094	chr6:30637998-30660611	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv884095	chr6:30644987-30664567	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
11	nsv884096	chr6:30647979-30664567	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv884097	chr6:30650378-30660611	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
13	nsv884098	chr6:30650378-30664567	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
14	nsv884099	chr6:30652931-30660611	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9262146	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9262146	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30655000-30658600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:30655000-30659200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr6:30655200-30657200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr6:30655200-30658200	Enhancers	Stomach Mucosa	stomach
5	chr6:30655400-30657000	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr6:30655400-30658400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr6:30655600-30657200	Flanking Active TSS	NHEK	skin
8	chr6:30655600-30658200	Flanking Active TSS	GM12878-XiMat	blood
9	chr6:30655600-30658400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:30655800-30657000	Transcr. at gene 5' and 3'	NHLF	lung
11	chr6:30655800-30657200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr6:30655800-30657200	Flanking Active TSS	HSMM	muscle
13	chr6:30655800-30657600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:30655800-30657800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:30655800-30657800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:30655800-30658000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:30655800-30658000	Enhancers	Fetal Brain Male	brain
18	chr6:30655800-30658000	Enhancers	Thymus	Thymus
19	chr6:30655800-30658200	Enhancers	Liver	Liver
20	chr6:30655800-30658200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:30655800-30658400	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr6:30656000-30657600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:30656000-30657800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr6:30656000-30657800	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr6:30656000-30657800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr6:30656000-30657800	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr6:30656000-30657800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:30656000-30657800	Weak transcription	Ovary	ovary
29	chr6:30656000-30658200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr6:30656000-30658200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr6:30656000-30658200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:30656000-30658400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr6:30656000-30658400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:30656000-30658600	Weak transcription	Aorta	Aorta
35	chr6:30656200-30657000	Enhancers	Small Intestine	intestine
36	chr6:30656200-30657200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:30656200-30657200	Weak transcription	Colonic Mucosa	Colon
38	chr6:30656200-30657200	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr6:30656200-30657200	Weak transcription	Right Atrium	heart
40	chr6:30656200-30657200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr6:30656200-30657400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:30656200-30657400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:30656200-30657400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr6:30656200-30657400	Weak transcription	A549	lung
45	chr6:30656200-30657400	Enhancers	K562	blood
46	chr6:30656200-30657400	Enhancers	NH-A	brain
47	chr6:30656200-30657600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:30656200-30657600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:30656200-30657600	Weak transcription	Brain Anterior Caudate	brain
50	chr6:30656200-30657600	Weak transcription	Fetal Intestine Small	intestine

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