Variant report

Variant	rs9887879
Chromosome Location	chr1:85744582-85744583
allele	G/T
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	MAX	chr1:85744399-85745029	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:85744501-85744819	HCT-116	colon:	n/a	n/a
3	JUND	chr1:85744546-85744971	A549	lung:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
4	POLR2A	chr1:85744494-85745030	HUVEC	blood vessel:	n/a	n/a
5	MAX	chr1:85744566-85744908	Hela-S3	cervix:	n/a	n/a
6	NFYA	chr1:85744535-85744862	Hela-S3	cervix:	n/a	chr1:85744678-85744692 chr1:85744678-85744696
7	CEBPB	chr1:85744524-85744895	A549	lung:	n/a	n/a
8	STAT5A	chr1:85744371-85744959	K562	blood:	n/a	n/a
9	POLR2A	chr1:85744554-85744911	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr1:85744456-85745017	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr1:85744532-85744908	Hela-S3	cervix:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
12	UBTF	chr1:85744526-85744974	K562	blood:	n/a	n/a
13	SMARCC1	chr1:85744532-85745314	Hela-S3	cervix:	n/a	n/a
14	JUN	chr1:85744425-85745740	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
15	MAFK	chr1:85744501-85745203	K562	blood:	n/a	chr1:85744729-85744738 chr1:85744729-85744739 chr1:85744742-85744757 chr1:85744689-85744700 chr1:85744618-85744633
16	JUND	chr1:85744329-85745186	HCT-116	colon:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
17	SIN3AK20	chr1:85744479-85745131	HCT-116	colon:	n/a	n/a
18	MAX	chr1:85744504-85744911	K562	blood:	n/a	n/a
19	FOS	chr1:85744472-85744944	MCF10A-Er-Src	breast:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
20	ELK1	chr1:85744545-85744994	Hela-S3	cervix:	n/a	n/a
21	FOSL2	chr1:85744493-85744872	MCF-7	breast:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
22	RXRA	chr1:85744404-85745081	SK-N-SH	brain:	n/a	chr1:85744539-85744552 chr1:85744540-85744551 chr1:85744539-85744552
23	POLR2A	chr1:85744460-85744944	K562	blood:	n/a	n/a
24	E2F4	chr1:85744465-85744940	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr1:85744472-85745015	HUVEC	blood vessel:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
26	MYC	chr1:85744519-85744926	MCF10A-Er-Src	breast:	n/a	n/a
27	FOSL2	chr1:85744423-85745009	A549	lung:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
28	TEAD4	chr1:85744328-85745031	K562	blood:	n/a	n/a
29	PBX3	chr1:85744331-85745079	SK-N-SH	brain:	n/a	n/a
30	JUN	chr1:85744483-85744956	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
31	IRF1	chr1:85744533-85744961	K562	blood:	n/a	chr1:85744731-85744740 chr1:85744622-85744631
32	TBL1XR1	chr1:85744403-85745019	K562	blood:	n/a	n/a
33	STAT3	chr1:85744494-85744983	MCF10A-Er-Src	breast:	n/a	n/a
34	EP300	chr1:85744538-85744974	Hela-S3	cervix:	n/a	n/a
35	JUND	chr1:85744322-85745112	SK-N-SH	brain:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
36	JUN	chr1:85744536-85744928	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
37	POLR2A	chr1:85744463-85744928	K562	blood:	n/a	n/a
38	GATA3	chr1:85744342-85745131	SK-N-SH	brain:	n/a	chr1:85744620-85744630 chr1:85744486-85744497 chr1:85744596-85744603
39	CEBPB	chr1:85744562-85745010	Hela-S3	cervix:	n/a	n/a
40	BATF	chr1:85744512-85744960	GM12878	blood:	n/a	chr1:85744727-85744738 chr1:85744745-85744756
41	JUND	chr1:85744410-85745015	K562	blood:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744747-85744758 chr1:85744731-85744739
42	FOS	chr1:85744532-85744940	MCF10A-Er-Src	breast:	n/a	chr1:85744747-85744758 chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739
43	SP1	chr1:85744309-85745181	HCT-116	colon:	n/a	chr1:85744679-85744700
44	MTA3	chr1:85744502-85745040	GM12878	blood:	n/a	n/a
45	TCF12	chr1:85744438-85745122	SK-N-SH	brain:	n/a	n/a
46	TCF12	chr1:85744313-85745100	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr1:85744386-85745051	SK-N-SH	brain:	n/a	n/a
48	CEBPB	chr1:85744565-85744908	K562	blood:	n/a	n/a
49	STAT3	chr1:85744536-85744924	MCF10A-Er-Src	breast:	n/a	n/a
50	JUN	chr1:85744515-85744977	HUVEC	blood vessel:	n/a	chr1:85744732-85744739 chr1:85744621-85744630 chr1:85744731-85744739

No.	Distal block	Cell Line	Cell type
1	chr1:85742187..85745018-chr1:85749555..85753087,3	K562	blood:
2	chr1:85743465..85746291-chr1:85746776..85749038,2	MCF-7	breast:
3	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
BCL10	TF binding region
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000264380	Chromatin interaction
ENSG00000142871	Chromatin interaction

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

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

rs_ID	r²[population]
rs1060843	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161564	0.92[ASN][1000 genomes]
rs11161581	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs11161583	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12065528	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12066982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12068389	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12068788	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12084232	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12086970	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12087340	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12562182	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12563515	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12726649	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12743302	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12744565	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs12746169	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17124345	0.92[ASN][1000 genomes]
rs35486093	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35783363	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35798604	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs36116171	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4074156	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4258258	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6693229	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9887811	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9887812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85742200-85744600	Weak transcription	Gastric	stomach
2	chr1:85742200-85744800	Weak transcription	Spleen	Spleen
3	chr1:85742800-85744600	Weak transcription	Pancreas	Pancrea
4	chr1:85742800-85744600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:85742800-85744600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:85742800-85763000	Weak transcription	Ovary	ovary
7	chr1:85743000-85744600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:85743000-85744600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:85743000-85744600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr1:85743000-85744600	Weak transcription	Fetal Kidney	kidney
11	chr1:85743000-85744600	Enhancers	HUVEC	blood vessel
12	chr1:85743000-85744800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:85743000-85745400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:85743000-85746000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr1:85743000-85747400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:85743000-85749200	Weak transcription	Fetal Stomach	stomach
17	chr1:85743000-85749200	Weak transcription	Psoas Muscle	Psoas
18	chr1:85743000-85773600	Weak transcription	Right Atrium	heart
19	chr1:85743200-85744600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:85743200-85744600	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr1:85743200-85744600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:85743200-85744600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:85743200-85744600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:85743200-85744600	Enhancers	Hela-S3	cervix
25	chr1:85743200-85744800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:85743200-85744800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:85743200-85744800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr1:85743200-85744800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:85743200-85744800	Weak transcription	Primary hematopoietic stem cells	blood
30	chr1:85743200-85744800	Weak transcription	Colonic Mucosa	Colon
31	chr1:85743200-85744800	Weak transcription	Esophagus	oesophagus
32	chr1:85743200-85744800	Weak transcription	Placenta	Placenta
33	chr1:85743200-85744800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:85743200-85744800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:85743200-85744800	Weak transcription	Right Ventricle	heart
36	chr1:85743200-85744800	Enhancers	HMEC	breast
37	chr1:85743200-85744800	Enhancers	NHEK	skin
38	chr1:85743200-85745000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:85743200-85745000	Weak transcription	Left Ventricle	heart
40	chr1:85743200-85745200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:85743200-85745200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:85743200-85745200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr1:85743200-85745800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:85743200-85747800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:85743200-85747800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr1:85743200-85747800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr1:85743200-85748000	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr1:85743200-85748200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr1:85743200-85752000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:85743400-85744600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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