Variant report

Variant	rs929042
Chromosome Location	chr6:28890800-28890801
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:265)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28890685-28892073	GM12878	blood:	n/a	n/a
2	HA-E2F1	chr6:28890604-28892095	MCF-7	breast:	n/a	chr6:28891750-28891760 chr6:28890907-28890921 chr6:28891800-28891809 chr6:28890959-28890971
3	POLR2A	chr6:28890484-28892149	ECC-1	luminal epithelium:	n/a	n/a
4	NR2F2	chr6:28889743-28892578	K562	blood:	n/a	n/a
5	MYBL2	chr6:28890481-28892204	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:28889875-28892268	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr6:28890358-28892615	K562	blood:	n/a	n/a
8	SMARCC1	chr6:28890501-28892027	Hela-S3	cervix:	n/a	n/a
9	HCFC1	chr6:28890274-28892322	Hela-S3	cervix:	n/a	n/a
10	GABPA	chr6:28890656-28891100	SK-N-SH	brain:	n/a	n/a
11	BCLAF1	chr6:28890539-28891191	GM12878	blood:	n/a	n/a
12	GABPA	chr6:28890768-28892170	K562	blood:	n/a	chr6:28891800-28891809
13	TAF1	chr6:28890697-28891067	PFSK-1	brain:	n/a	n/a
14	ATF2	chr6:28890723-28891520	GM12878	blood:	n/a	n/a
15	SPI1	chr6:28890793-28890971	K562	blood:	n/a	n/a
16	POLR2A	chr6:28890690-28892256	HepG2	liver:	n/a	n/a
17	POU2F2	chr6:28890710-28891074	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:28890756-28892067	A549	lung:	n/a	n/a
19	POLR2A	chr6:28890378-28892039	GM12891	blood:	n/a	n/a
20	BHLHE40	chr6:28890684-28892055	GM12878	blood:	n/a	chr6:28891990-28892006 chr6:28891987-28892003
21	PML	chr6:28889740-28892185	K562	blood:	n/a	chr6:28890027-28890036
22	TAF1	chr6:28890629-28891127	PFSK-1	brain:	n/a	n/a
23	MXI1	chr6:28889872-28892194	IMR90	lung:	n/a	n/a
24	CHD2	chr6:28890786-28891210	K562	blood:	n/a	n/a
25	POLR2A	chr6:28889681-28892110	K562	blood:	n/a	n/a
26	ELK1	chr6:28890567-28890904	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:28889280-28892096	K562	blood:	n/a	n/a
28	SPI1	chr6:28890637-28891159	GM12891	blood:	n/a	n/a
29	POLR2A	chr6:28890796-28892070	H1-hESC	embryonic stem cell:	n/a	n/a
30	CREB1	chr6:28890714-28890903	A549	lung:	n/a	n/a
31	ZNF263	chr6:28889915-28892045	HEK293-T-REx	kidney:	n/a	n/a
32	POU2F2	chr6:28890729-28891407	GM12891	blood:	n/a	n/a
33	MAX	chr6:28890653-28892072	GM12878	blood:	n/a	n/a
34	CCNT2	chr6:28890492-28892028	K562	blood:	n/a	chr6:28891766-28891775 chr6:28890781-28890790 chr6:28891800-28891809
35	POLR2A	chr6:28889873-28892186	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr6:28890298-28892108	GM15510	blood:	n/a	n/a
37	POLR2A	chr6:28890719-28892101	HepG2	liver:	n/a	n/a
38	POLR2A	chr6:28889258-28892112	HepG2	liver:	n/a	n/a
39	POLR2A	chr6:28889870-28892107	PBDE	blood:	n/a	n/a
40	TAF1	chr6:28890648-28892188	H1-hESC	embryonic stem cell:	n/a	n/a
41	MYC	chr6:28889871-28892047	K562	blood:	n/a	chr6:28890440-28890449 chr6:28890026-28890035 chr6:28890025-28890034
42	GABPA	chr6:28890605-28891070	A549	lung:	n/a	n/a
43	POLR2A	chr6:28889737-28892105	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr6:28890128-28892096	GM12878	blood:	n/a	n/a
45	ELF1	chr6:28890743-28892492	GM12878	blood:	n/a	chr6:28891798-28891810 chr6:28891752-28891761
46	SIN3AK20	chr6:28890731-28891084	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr6:28890769-28892087	ECC-1	luminal epithelium:	n/a	n/a
48	POLR2A	chr6:28889355-28892105	GM12878	blood:	n/a	n/a
49	POLR2A	chr6:28886841-28892929	HepG2	liver:	n/a	n/a
50	POLR2A	chr6:28890310-28892159	H1-neurons	neurons:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:73874220..73874999-chr6:28890150..28891088,2	Hela-S3	cervix:
2	chr6:28887886..28894013-chr6:28935014..28940220,8	K562	blood:
3	chr6:28831130..28836886-chr6:28890033..28892870,9	MCF-7	breast:
4	chr6:28889368..28892748-chr6:28952347..28956108,5	MCF-7	breast:
5	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
6	chr6:28874441..28877573-chr6:28886876..28891614,6	MCF-7	breast:
7	chr6:28890449..28893259-chr6:28971754..28975345,6	K562	blood:
8	chr6:28889372..28892274-chr6:28936954..28941148,4	K562	blood:
9	chr6:28889101..28891643-chr6:29595051..29597893,2	K562	blood:
10	chr6:28890727..28894097-chr6:28943047..28947323,5	MCF-7	breast:
11	chr6:28831640..28835125-chr6:28890004..28893108,3	MCF-7	breast:
12	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:
13	chr6:28882946..28884920-chr6:28890308..28891920,2	MCF-7	breast:
14	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
15	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
16	chr6:28805285..28808440-chr6:28888511..28892745,5	K562	blood:
17	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
18	chr6:27776463..27779000-chr6:28890031..28892525,2	MCF-7	breast:
19	chr6:28890160..28893119-chr6:28970726..28976038,6	K562	blood:
20	chr6:28805285..28809041-chr6:28890242..28892830,8	K562	blood:
21	chr22:29137920..29138552-chr6:28890584..28891243,3	Hela-S3	cervix:
22	chr6:28831633..28833233-chr6:28890419..28893119,2	K562	blood:
23	chr6:28856776..28858832-chr6:28890243..28892379,2	MCF-7	breast:
24	chr6:27831507..27834483-chr6:28890233..28891763,2	MCF-7	breast:
25	chr6:28804571..28808832-chr6:28889803..28892525,4	MCF-7	breast:

No data

Variant related genes	Relation type
TRIM27	TF binding region
ENSG00000198374	Chromatin interaction
ENSG00000183765	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000212240	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000228666	Chromatin interaction
ENSG00000204681	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000244349	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000217646	Chromatin interaction
ENSG00000100209	Chromatin interaction
ENSG00000132481	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000233366	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10484543	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1061625	0.88[ASN][1000 genomes]
rs172326	0.89[ASN][1000 genomes]
rs1794588	0.87[ASN][1000 genomes]
rs184094	0.83[ASN][1000 genomes]
rs209127	0.86[ASN][1000 genomes]
rs209140	0.91[ASN][1000 genomes]
rs209147	0.86[ASN][1000 genomes]
rs209151	0.87[ASN][1000 genomes]
rs209165	0.84[ASN][1000 genomes]
rs209172	0.83[ASN][1000 genomes]
rs209177	0.84[ASN][1000 genomes]
rs209180	0.81[ASN][1000 genomes]
rs2097424	0.86[ASN][1000 genomes]
rs2148007	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2269553	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28381661	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28381663	0.81[ASN][1000 genomes]
rs28400868	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28400869	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs28743260	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2894066	0.88[ASN][1000 genomes]
rs3131067	0.81[ASN][1000 genomes]
rs3132377	0.88[ASN][1000 genomes]
rs3132380	0.83[ASN][1000 genomes]
rs3135314	0.81[ASN][1000 genomes]
rs413972	0.89[ASN][1000 genomes]
rs422331	0.83[ASN][1000 genomes]
rs429369	0.88[ASN][1000 genomes]
rs4484511	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6909419	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6912843	0.82[ASN][1000 genomes]
rs743847	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7750338	0.88[ASN][1000 genomes]
rs7763940	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7769221	0.88[ASN][1000 genomes]
rs7776376	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs876737	0.81[ASN][1000 genomes]
rs9257269	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257270	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9257274	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257280	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9257281	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257328	0.88[ASN][1000 genomes]
rs9257424	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9348814	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9368576	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9378149	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393932	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9393933	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9404976	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:159 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28889200-28890800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
2	chr6:28889200-28890800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
3	chr6:28889200-28890800	Transcr. at gene 5' and 3'	K562	blood
4	chr6:28889200-28891400	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr6:28889400-28890800	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
6	chr6:28889400-28890800	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr6:28889600-28890800	Flanking Active TSS	Fetal Brain Female	brain
8	chr6:28889800-28890800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
9	chr6:28889800-28890800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr6:28889800-28890800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr6:28889800-28890800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:28889800-28890800	Flanking Active TSS	Brain Angular Gyrus	brain
13	chr6:28889800-28890800	Flanking Active TSS	Brain Anterior Caudate	brain
14	chr6:28889800-28890800	Flanking Active TSS	Brain Hippocampus Middle	brain
15	chr6:28889800-28892400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:28889800-28892600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:28890000-28890800	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr6:28890000-28890800	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr6:28890000-28890800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
20	chr6:28890000-28890800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr6:28890000-28890800	Flanking Active TSS	Fetal Thymus	thymus
22	chr6:28890000-28891000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr6:28890000-28891000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:28890000-28891200	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr6:28890000-28891200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:28890000-28891400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr6:28890000-28892200	Active TSS	Aorta	Aorta
28	chr6:28890000-28892200	Active TSS	Fetal Intestine Small	intestine
29	chr6:28890000-28892400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:28890000-28892400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr6:28890000-28892400	Active TSS	Colonic Mucosa	Colon
32	chr6:28890000-28892400	Active TSS	Fetal Intestine Large	intestine
33	chr6:28890000-28892600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:28890000-28892600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:28890000-28892600	Active TSS	Lung	lung
36	chr6:28890000-28892600	Active TSS	Pancreas	Pancrea
37	chr6:28890000-28892600	Active TSS	Psoas Muscle	Psoas
38	chr6:28890000-28892800	Active TSS	H9 Cell Line	embryonic stem cell
39	chr6:28890000-28892800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:28890200-28890800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:28890200-28890800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:28890200-28890800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr6:28890200-28890800	Flanking Active TSS	Fetal Brain Male	brain
44	chr6:28890200-28890800	Active TSS	Right Atrium	heart
45	chr6:28890200-28890800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr6:28890200-28891000	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr6:28890200-28891800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:28890200-28892000	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr6:28890200-28892000	Active TSS	Fetal Muscle Trunk	muscle
50	chr6:28890200-28892000	Active TSS	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links