Variant report

Variant	rs16836586
Chromosome Location	chr1:154947905-154947906
allele	A/G
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	ARID3A	chr1:154946050-154947931	HepG2	liver:	n/a	n/a
2	MAX	chr1:154946032-154948395	K562	blood:	n/a	n/a
3	POLR2A	chr1:154945991-154949108	K562	blood:	n/a	n/a
4	CHD2	chr1:154947904-154948435	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:154944609-154948507	HUVEC	blood vessel:	n/a	n/a
6	SIN3AK20	chr1:154946945-154948400	K562	blood:	n/a	n/a
7	POLR2A	chr1:154944669-154948429	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr1:154946126-154948479	GM18951	blood:	n/a	n/a
9	MYC	chr1:154946031-154948503	MCF10A-Er-Src	breast:	n/a	n/a
10	ZC3H11A	chr1:154947681-154948353	K562	blood:	n/a	n/a
11	MAX	chr1:154945998-154948303	A549	lung:	n/a	n/a
12	POLR2A	chr1:154940758-154948467	HepG2	liver:	n/a	n/a
13	IRF1	chr1:154946045-154948432	K562	blood:	n/a	chr1:154948298-154948311 chr1:154948296-154948310 chr1:154946328-154946342 chr1:154948301-154948312 chr1:154948294-154948315 chr1:154946232-154946246 chr1:154946312-154946326 chr1:154946623-154946637 chr1:154948300-154948311 chr1:154948298-154948311 chr1:154948302-154948312 chr1:154946923-154946932 chr1:154948298-154948312 chr1:154948299-154948312 chr1:154948299-154948313 chr1:154948299-154948313 chr1:154948298-154948311 chr1:154947352-154947361 chr1:154946132-154946142 chr1:154948297-154948311
14	CEBPB	chr1:154946020-154948730	Hela-S3	cervix:	n/a	chr1:154947053-154947061
15	NRF1	chr1:154945891-154948500	SK-N-SH	brain:	n/a	chr1:154947428-154947439 chr1:154947430-154947439 chr1:154947372-154947383 chr1:154948243-154948252 chr1:154947428-154947439 chr1:154947428-154947442 chr1:154947115-154947124 chr1:154947428-154947437
16	MAX	chr1:154946703-154948212	K562	blood:	n/a	n/a
17	MAX	chr1:154945998-154948398	MCF-7	breast:	n/a	n/a
18	CUX1	chr1:154947176-154948090	K562	blood:	n/a	n/a
19	RELA	chr1:154946146-154948316	GM18951	blood:	n/a	n/a
20	POLR2A	chr1:154945898-154948805	K562	blood:	n/a	n/a
21	POLR2A	chr1:154946045-154948572	GM12892	blood:	n/a	n/a
22	MAZ	chr1:154946044-154948417	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:154944760-154948847	HepG2	liver:	n/a	n/a
24	SP1	chr1:154945834-154948495	A549	lung:	n/a	chr1:154947738-154947748 chr1:154948172-154948184 chr1:154946625-154946634 chr1:154946312-154946324 chr1:154947099-154947120 chr1:154946922-154946943 chr1:154946328-154946340 chr1:154946328-154946340 chr1:154948242-154948254 chr1:154946891-154946905 chr1:154946498-154946510 chr1:154948244-154948253 chr1:154948243-154948252 chr1:154946961-154946982 chr1:154948174-154948183 chr1:154946312-154946324 chr1:154948242-154948254 chr1:154946234-154946243 chr1:154948172-154948184 chr1:154948239-154948253 chr1:154946313-154946323 chr1:154946270-154946279 chr1:154946427-154946441 chr1:154946232-154946244 chr1:154946820-154946834 chr1:154946330-154946339 chr1:154946233-154946243 chr1:154946590-154946604 chr1:154947739-154947748 chr1:154948173-154948182 chr1:154947738-154947748 chr1:154946232-154946244 chr1:154946623-154946635 chr1:154947051-154947072 chr1:154946499-154946508 chr1:154946313-154946323 chr1:154946495-154946509 chr1:154948243-154948253 chr1:154946233-154946243
25	POLR2A	chr1:154945983-154948190	HCT-116	colon:	n/a	n/a
26	POLR2A	chr1:154946197-154948506	GM15510	blood:	n/a	n/a
27	POLR2A	chr1:154946042-154948839	GM12891	blood:	n/a	n/a
28	NRF1	chr1:154946651-154947957	GM12878	blood:	n/a	chr1:154947428-154947439 chr1:154947430-154947439 chr1:154947372-154947383 chr1:154947428-154947439 chr1:154947428-154947442 chr1:154947115-154947124 chr1:154947428-154947437
29	BCL3	chr1:154945843-154948226	A549	lung:	n/a	chr1:154948173-154948182 chr1:154946852-154946861 chr1:154946330-154946339 chr1:154946647-154946656
30	WRNIP1	chr1:154946711-154948206	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:154946130-154948517	GM19099	blood:	n/a	n/a
32	POLR2A	chr1:154945968-154948653	GM12878	blood:	n/a	n/a
33	GABPA	chr1:154945955-154947936	A549	lung:	n/a	chr1:154947428-154947439 chr1:154947430-154947439 chr1:154947428-154947442 chr1:154947115-154947124 chr1:154947428-154947437
34	POLR2A	chr1:154944875-154948692	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr1:154946181-154948437	Raji	blood:	n/a	n/a
36	RELA	chr1:154946180-154948452	GM10847	blood:	n/a	n/a
37	TAF1	chr1:154945930-154948017	A549	lung:	n/a	n/a
38	MXI1	chr1:154946012-154948385	HepG2	liver:	n/a	n/a
39	POLR2A	chr1:154945872-154949046	HCT-116	colon:	n/a	n/a
40	MAX	chr1:154945922-154948533	K562	blood:	n/a	n/a
41	MAX	chr1:154945988-154948419	ECC-1	luminal epithelium:	n/a	n/a
42	STAT5A	chr1:154945939-154948360	GM12878	blood:	n/a	chr1:154948300-154948311 chr1:154946599-154946619 chr1:154948245-154948257
43	MYC	chr1:154945990-154948070	MCF10A-Er-Src	breast:	n/a	n/a
44	JUN	chr1:154946026-154948449	K562	blood:	n/a	chr1:154946685-154946696 chr1:154946687-154946699 chr1:154946688-154946698 chr1:154948175-154948184 chr1:154946689-154946698 chr1:154946688-154946698 chr1:154946688-154946698 chr1:154946718-154946726 chr1:154947054-154947063 chr1:154946964-154946973 chr1:154946688-154946698
45	MAX	chr1:154946127-154948008	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr1:154945955-154948623	GM12892	blood:	n/a	n/a
47	BHLHE40	chr1:154946095-154948422	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:154945974-154948440	MCF-7	breast:	n/a	n/a
49	RELA	chr1:154946136-154948439	GM19099	blood:	n/a	n/a
50	SIN3A	chr1:154946119-154948958	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154947408..154948016-chr2:10262107..10263095,2	Hela-S3	cervix:
2	chr1:154943492..154949367-chr1:155033837..155038035,9	MCF-7	breast:
3	chr1:28975060..28975678-chr1:154947800..154948336,2	Hela-S3	cervix:
4	chr1:154944220..154948259-chr1:155103576..155107473,5	MCF-7	breast:
5	chr1:154947073..154947932-chr17:56756404..56757331,2	Hela-S3	cervix:
6	chr1:154946748..154948296-chr1:155227059..155229711,2	MCF-7	breast:
7	chr1:154573844..154576580-chr1:154947411..154949636,2	K562	blood:
8	chr1:154947750..154948647-chr17:26989112..26989753,2	Hela-S3	cervix:
9	chr1:154945666..154948498-chr1:155033358..155037574,4	K562	blood:
10	chr1:154947156..154950628-chr1:155023259..155025337,3	MCF-7	breast:
11	chr1:154943580..154949331-chr1:155014649..155018913,6	MCF-7	breast:
12	chr1:11968639..11970236-chr1:154947682..154949521,2	K562	blood:
13	chr1:154947106..154947985-chr11:6624525..6625065,2	HCT-116	colon:
14	chr1:154947155..154947908-chr16:14726145..14726861,2	Hela-S3	cervix:
15	chr1:154944682..154948805-chr1:155021065..155026491,10	K562	blood:
16	chr1:154944693..154948498-chr1:155033358..155037574,5	K562	blood:

Variant related genes	Relation type
CKS1B	TF binding region
MIR4258	TF binding region
SHC1	TF binding region
ENSG00000171848	Chromatin interaction
ENSG00000132581	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000132275	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000140694	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000103429	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000166333	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000109111	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000270103	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11465203	1.00[AMR][1000 genomes]
rs16836580	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs2070679	1.00[AMR][1000 genomes]
rs2089247	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs2878517	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs6661212	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs6671228	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs6683147	1.00[AMR][1000 genomes]
rs6683706	1.00[AMR][1000 genomes]
rs6695407	1.00[YRI][hapmap]
rs6698284	1.00[AMR][1000 genomes]
rs7528548	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs7549705	1.00[YRI][hapmap];1.00[AMR][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	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154941000-154949000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr1:154944200-154948800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:154944600-154948200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr1:154944600-154948400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:154944600-154948800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:154945000-154948600	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:154945000-154949200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:154945400-154948800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:154945600-154948400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:154945600-154948600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:154945600-154948600	Active TSS	Aorta	Aorta
12	chr1:154945600-154948600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr1:154945600-154948800	Active TSS	A549	lung
14	chr1:154945600-154949000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:154945600-154949000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:154945800-154948200	Active TSS	Brain Germinal Matrix	brain
17	chr1:154945800-154948200	Active TSS	Psoas Muscle	Psoas
18	chr1:154945800-154948200	Bivalent/Poised TSS	HepG2	liver
19	chr1:154945800-154948400	Active TSS	Fetal Heart	heart
20	chr1:154945800-154948400	Active TSS	Fetal Lung	lung
21	chr1:154945800-154948600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:154945800-154948600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:154945800-154948600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:154945800-154948600	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr1:154945800-154948600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:154945800-154948600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:154945800-154948600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:154945800-154948600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:154945800-154948600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:154945800-154948600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:154945800-154948600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:154945800-154948600	Active TSS	Colonic Mucosa	Colon
33	chr1:154945800-154948600	Active TSS	Duodenum Mucosa	Duodenum
34	chr1:154945800-154948600	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:154945800-154948600	Active TSS	Fetal Kidney	kidney
36	chr1:154945800-154948600	Active TSS	Pancreas	Pancrea
37	chr1:154945800-154948600	Active TSS	Right Atrium	heart
38	chr1:154945800-154948600	Active TSS	Right Ventricle	heart
39	chr1:154945800-154948600	Active TSS	Hela-S3	cervix
40	chr1:154945800-154948600	Active TSS	HMEC	breast
41	chr1:154945800-154948600	Active TSS	HUVEC	blood vessel
42	chr1:154945800-154948600	Active TSS	K562	blood
43	chr1:154945800-154948800	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:154945800-154948800	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:154945800-154948800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:154945800-154948800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:154945800-154948800	Active TSS	Esophagus	oesophagus
48	chr1:154945800-154948800	Active TSS	Fetal Intestine Large	intestine
49	chr1:154945800-154948800	Active TSS	Stomach Mucosa	stomach
50	chr1:154945800-154948800	Active TSS	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links