Variant report

Variant	rs12211927
Chromosome Location	chr6:28602631-28602632
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:183)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:28602339-28603469	A549	lung:	n/a	n/a
2	POLR2A	chr6:28602466-28603550	H1-neurons	neurons:	n/a	n/a
3	HDAC2	chr6:28602313-28602718	HepG2	liver:	n/a	n/a
4	NFIC	chr6:28602233-28602746	ECC-1	luminal epithelium:	n/a	n/a
5	MXI1	chr6:28602158-28604100	SK-N-SH	brain:	n/a	n/a
6	ZNF263	chr6:28601986-28604212	HEK293-T-REx	kidney:	n/a	n/a
7	HNF4A	chr6:28602427-28602705	HepG2	liver:	n/a	chr6:28602549-28602564 chr6:28602550-28602562 chr6:28602548-28602563 chr6:28602550-28602563 chr6:28602550-28602562 chr6:28602551-28602563 chr6:28602550-28602562 chr6:28602550-28602562
8	POLR2A	chr6:28602605-28602675	Gliobla	brain:	n/a	n/a
9	FOXA1	chr6:28602296-28602637	HepG2	liver:	n/a	n/a
10	MAFK	chr6:28602488-28602788	HepG2	liver:	n/a	n/a
11	REST	chr6:28602233-28603859	H1-neurons	neurons:	n/a	chr6:28603707-28603717
12	CTCF	chr6:28602620-28602770	HPF	lung:	n/a	n/a
13	NFIC	chr6:28602149-28602921	ECC-1	luminal epithelium:	n/a	n/a
14	CEBPB	chr6:28602567-28602667	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr6:28602553-28602665	A549	lung:	n/a	n/a
16	POLR2A	chr6:28602411-28603489	H1-neurons	neurons:	n/a	n/a
17	KAP1	chr6:28601523-28602919	U2OS	brain:	n/a	n/a
18	HNF4A	chr6:28602301-28602703	HepG2	liver:	n/a	chr6:28602549-28602564 chr6:28602550-28602562 chr6:28602548-28602563 chr6:28602550-28602563 chr6:28602550-28602562 chr6:28602551-28602563 chr6:28602550-28602562 chr6:28602550-28602562
19	POLR2A	chr6:28602331-28603480	SK-N-MC	brain:	n/a	n/a
20	KAP1	chr6:28601225-28603443	HEK293	kidney:	n/a	n/a
21	SIN3A	chr6:28602282-28603885	H1-hESC	embryonic stem cell:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:28602584-28602634	SK-N-SH_RA	brain:	n/a
2	chr6:28602584-28602634	RPTEC	kidney:	n/a
3	chr6:28602626-28602676	GM06990	blood:	n/a
4	chr6:28602619-28602669	Jurkat	blood:	n/a
5	chr6:28602584-28602634	HRCEpiC	kidney:	n/a
6	chr6:28602584-28602634	U87	brain:	n/a
7	chr6:28602584-28602634	NT2-D1	testis:	n/a
8	chr6:28602626-28602676	Caco-2	colon:	n/a
9	chr6:28602584-28602634	GM06990	blood:	n/a
10	chr6:28602584-28602634	PrEC	prostate:	n/a
11	chr6:28602619-28602669	AG09319	gingival:	n/a
12	chr6:28602584-28602634	AG04450	lung:	fetal
13	chr6:28602619-28602669	NH-A	brain:	n/a
14	chr6:28602626-28602676	ovcar-3	ovarian:	n/a
15	chr6:28602619-28602669	HMEC	breast:	n/a
16	chr6:28602626-28602676	HRE	kidney:	n/a
17	chr6:28602619-28602669	BE2_C	brain:	n/a
18	chr6:28602619-28602669	HRE	kidney:	n/a
19	chr6:28602619-28602669	HL-60	blood:	n/a
20	chr6:28602626-28602676	HCM	heart:	n/a
21	chr6:28602584-28602634	AG09319	gingival:	n/a
22	chr6:28602619-28602669	GM06990	blood:	n/a
23	chr6:28602626-28602676	K562	blood:	n/a
24	chr6:28602619-28602669	GM12891	blood:	n/a
25	chr6:28602584-28602634	SAEC	small airway:	n/a
26	chr6:28602584-28602634	HCPEpiC	choroid plexus:	n/a
27	chr6:28602619-28602669	HepG2	liver:	n/a
28	chr6:28602626-28602676	GM12878	blood:	n/a
29	chr6:28602584-28602634	SKMC	muscle:	n/a
30	chr6:28602626-28602676	GM19239	blood:	n/a
31	chr6:28602626-28602676	Hela-S3	cervix:	n/a
32	chr6:28602619-28602669	NHBE	bronchial:	n/a
33	chr6:28602626-28602676	SAEC	small airway:	n/a
34	chr6:28602619-28602669	AG04450	lung:	fetal
35	chr6:28602626-28602676	PrEC	prostate:	n/a
36	chr6:28602619-28602669	SAEC	small airway:	n/a
37	chr6:28602619-28602669	HCF	heart:	n/a
38	chr6:28602626-28602676	NHDF-neo	bronchial:	n/a
39	chr6:28602584-28602634	GM12878	blood:	n/a
40	chr6:28602626-28602676	MCF10A-Er-Src	breast:	n/a
41	chr6:28602584-28602634	ovcar-3	ovarian:	n/a
42	chr6:28602626-28602676	HL-60	blood:	n/a
43	chr6:28602619-28602669	HRPEpiC	eye:	n/a
44	chr6:28602584-28602634	AG04449	skin:	fetal
45	chr6:28602619-28602669	GM12892	blood:	n/a
46	chr6:28602626-28602676	HNPCEpiC	eye:	n/a
47	chr6:28602626-28602676	AG04449	skin:	fetal
48	chr6:28602584-28602634	HEK293	kidney:	embryo
49	chr6:28602619-28602669	K562	blood:	n/a
50	chr6:28602584-28602634	Hepatocyte	liver:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28582156..28586237-chr6:28601069..28603430,3	K562	blood:
2	chr6:28598566..28600689-chr6:28601579..28603852,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000271440	TF binding region
ENSG00000271440	CpG island
ENSG00000232040	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12180700	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1319075	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1810619	0.95[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2394149	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs370520	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs380914	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs414205	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs420478	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4289643	0.80[ASN][1000 genomes]
rs436827	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs450630	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6456825	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6925714	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926221	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926470	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7382146	0.81[EUR][1000 genomes]
rs9295772	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9295773	0.82[EUR][1000 genomes]
rs9348810	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9368568	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378185	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380079	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9380083	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9393920	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393921	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9501180	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9885928	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[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	nsv1020689	chr6:28449137-28635171	Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv830621	chr6:28473951-28675709	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv1031671	chr6:28575172-28678126	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28601000-28604000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:28601200-28603200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:28601200-28603800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:28601200-28603800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:28601200-28604000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:28601400-28604000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr6:28601600-28603600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr6:28601600-28604200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr6:28602200-28603200	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr6:28602200-28603600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:28602200-28604000	Active TSS	Brain Anterior Caudate	brain
12	chr6:28602200-28604000	Active TSS	A549	lung
13	chr6:28602200-28604000	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr6:28602200-28604200	Bivalent/Poised TSS	Brain Angular Gyrus	brain
15	chr6:28602400-28602800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:28602400-28602800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
17	chr6:28602400-28602800	Active TSS	Brain Germinal Matrix	brain
18	chr6:28602400-28602800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
19	chr6:28602400-28602800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr6:28602400-28603000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:28602400-28603000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:28602400-28603000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
23	chr6:28602400-28603000	Bivalent/Poised TSS	Osteobl	bone
24	chr6:28602400-28603200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:28602400-28603200	Active TSS	HSMMtube	muscle
26	chr6:28602400-28603400	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:28602400-28603400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
28	chr6:28602400-28603400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
29	chr6:28602400-28603400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:28602400-28603400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:28602400-28603400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
32	chr6:28602400-28603400	Bivalent/Poised TSS	NHDF-Ad	bronchial
33	chr6:28602400-28603400	Flanking Bivalent TSS/Enh	NHEK	skin
34	chr6:28602400-28603400	Bivalent/Poised TSS	NHLF	lung
35	chr6:28602400-28603600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:28602400-28603600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:28602400-28603600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
38	chr6:28602400-28603600	Active TSS	Fetal Lung	lung
39	chr6:28602400-28603600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
40	chr6:28602400-28603800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:28602400-28603800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:28602400-28603800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:28602400-28603800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:28602400-28603800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:28602400-28603800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr6:28602400-28603800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
47	chr6:28602400-28603800	Bivalent/Poised TSS	HSMM	muscle
48	chr6:28602400-28603800	Bivalent/Poised TSS	NH-A	brain
49	chr6:28602400-28604000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:28602400-28604000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links