Variant report

Variant	rs436827
Chromosome Location	chr6:28557133-28557134
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:236)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:236 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr6:28556995-28557561	A549	lung:	n/a	n/a
2	YY1	chr6:28557002-28557567	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr6:28556917-28557666	ECC-1	luminal epithelium:	n/a	n/a
4	EP300	chr6:28557001-28557386	GM12878	blood:	n/a	n/a
5	TCF7L2	chr6:28557003-28557539	HCT-116	colon:	n/a	n/a
6	MAX	chr6:28557108-28557684	SK-N-SH	brain:	n/a	n/a
7	ZKSCAN1	chr6:28557004-28557602	Hela-S3	cervix:	n/a	n/a
8	TBP	chr6:28556918-28557456	H1-hESC	embryonic stem cell:	n/a	n/a
9	BHLHE40	chr6:28556999-28557493	HepG2	liver:	n/a	n/a
10	SIN3A	chr6:28556860-28558249	H1-hESC	embryonic stem cell:	n/a	n/a
11	ARID3A	chr6:28556957-28557603	HepG2	liver:	n/a	n/a
12	MAX	chr6:28557040-28557644	HepG2	liver:	n/a	n/a
13	RCOR1	chr6:28556973-28557589	HepG2	liver:	n/a	n/a
14	EBF1	chr6:28556955-28557365	GM12878	blood:	n/a	n/a
15	TBP	chr6:28556902-28557457	HepG2	liver:	n/a	n/a
16	MAX	chr6:28556965-28557732	ECC-1	luminal epithelium:	n/a	n/a
17	EP300	chr6:28557004-28557481	H1-hESC	embryonic stem cell:	n/a	n/a
18	MYC	chr6:28557127-28557147	HUVEC	blood vessel:	n/a	n/a
19	HDAC2	chr6:28556919-28557617	HepG2	liver:	n/a	n/a
20	MYC	chr6:28557016-28557665	MCF10A-Er-Src	breast:	n/a	n/a
21	MAX	chr6:28556907-28557724	MCF-7	breast:	n/a	n/a
22	POU2F2	chr6:28557064-28557244	GM12878	blood:	n/a	n/a
23	EBF1	chr6:28557082-28557262	GM12878	blood:	n/a	n/a
24	CEBPB	chr6:28557010-28557705	HepG2	liver:	n/a	n/a
25	HNF4A	chr6:28556983-28557444	HepG2	liver:	n/a	chr6:28557181-28557196
26	RXRA	chr6:28556984-28557461	HepG2	liver:	n/a	n/a
27	CREB1	chr6:28557111-28557360	A549	lung:	n/a	n/a
28	ELK1	chr6:28556974-28557439	Hela-S3	cervix:	n/a	n/a
29	HNF4G	chr6:28556828-28557443	HepG2	liver:	n/a	chr6:28557182-28557197
30	TCF7L2	chr6:28556960-28557752	PANC-1	pancreas:	n/a	n/a
31	POLR2A	chr6:28556950-28557584	H1-hESC	embryonic stem cell:	n/a	n/a
32	ATF2	chr6:28556906-28557795	H1-hESC	embryonic stem cell:	n/a	n/a
33	TAF7	chr6:28556963-28557693	H1-hESC	embryonic stem cell:	n/a	n/a
34	WRNIP1	chr6:28556999-28557484	GM12878	blood:	n/a	n/a
35	TAF1	chr6:28557004-28557483	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr6:28556886-28557690	HCT-116	colon:	n/a	n/a
37	MAZ	chr6:28557051-28557534	Hela-S3	cervix:	n/a	n/a
38	USF1	chr6:28557054-28557474	A549	lung:	n/a	n/a
39	NFIC	chr6:28556958-28557602	HepG2	liver:	n/a	n/a
40	GATA3	chr6:28557004-28557680	MCF-7	breast:	n/a	n/a
41	TCF12	chr6:28557040-28557281	GM12878	blood:	n/a	n/a
42	ZBTB33	chr6:28556932-28557612	A549	lung:	n/a	n/a
43	TEAD4	chr6:28556939-28557558	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAX	chr6:28556991-28557623	H1-hESC	embryonic stem cell:	n/a	n/a
45	ETS1	chr6:28556984-28557601	A549	lung:	n/a	n/a
46	CTCF	chr6:28557120-28557270	HPAF	blood vessel:	n/a	n/a
47	ETS1	chr6:28556905-28557742	A549	lung:	n/a	n/a
48	TBP	chr6:28556937-28557354	GM12878	blood:	n/a	n/a
49	MAFK	chr6:28556944-28557527	H1-hESC	embryonic stem cell:	n/a	n/a
50	SIN3AK20	chr6:28556737-28557835	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28556555..28559076-chr6:28582763..28585041,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPX5-1	chr6:28557006-28559524	XLOC_005223

No data

Variant related genes	Relation type
SCAND3	TF binding region
ENSG00000232040	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12180700	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12211927	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1319075	0.81[ASN][1000 genomes]
rs1810619	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2394149	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs370520	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380914	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs414205	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs420478	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4289643	0.84[ASN][1000 genomes]
rs450630	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456825	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925714	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6926221	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6926470	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295772	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9295773	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9348810	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9368568	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9378185	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9380079	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380083	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393920	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9393921	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9501180	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9885928	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462666	chr6:28417222-28574415	Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv601210	chr6:28417222-28574415	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28552400-28559600	Strong transcription	K562	blood
2	chr6:28553000-28558200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:28553200-28558200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:28553200-28558600	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr6:28553800-28557600	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:28553800-28558200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr6:28553800-28558400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr6:28553800-28558400	Active TSS	H1 Cell Line	embryonic stem cell
9	chr6:28554000-28558000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
10	chr6:28554400-28558400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28554400-28558400	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr6:28554600-28557200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:28555400-28557200	Weak transcription	Spleen	Spleen
14	chr6:28555600-28557200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:28555600-28557400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:28555800-28557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28555800-28557200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:28555800-28557200	Weak transcription	Right Ventricle	heart
19	chr6:28555800-28557200	Enhancers	Osteobl	bone
20	chr6:28555800-28557400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:28555800-28557400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:28555800-28557400	Weak transcription	Pancreas	Pancrea
23	chr6:28556000-28557200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:28556000-28558000	Enhancers	HMEC	breast
25	chr6:28556000-28558200	Active TSS	Fetal Brain Female	brain
26	chr6:28556200-28557200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:28556200-28557200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:28556200-28558400	Active TSS	H9 Cell Line	embryonic stem cell
29	chr6:28556400-28557200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:28556400-28557200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr6:28556400-28558200	Active TSS	A549	lung
32	chr6:28556600-28558000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:28556800-28557200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:28556800-28557200	Bivalent Enhancer	Fetal Heart	heart
35	chr6:28556800-28557200	Active TSS	Fetal Intestine Large	intestine
36	chr6:28556800-28557200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
37	chr6:28556800-28557200	Active TSS	Fetal Stomach	stomach
38	chr6:28556800-28557400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
39	chr6:28556800-28557400	Active TSS	NHLF	lung
40	chr6:28556800-28557600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:28556800-28557600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr6:28556800-28557600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:28556800-28557600	Flanking Active TSS	GM12878-XiMat	blood
44	chr6:28556800-28557800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:28556800-28558000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:28556800-28558000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:28556800-28558000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
48	chr6:28556800-28558000	Active TSS	Brain Germinal Matrix	brain
49	chr6:28556800-28558000	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:28556800-28558000	Flanking Active TSS	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links