Variant report

Variant	rs6658104
Chromosome Location	chr1:59364918-59364919
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:181)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:181 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TRIM28	chr1:59364460-59365503	K562	blood:	n/a	n/a
2	MAX	chr1:59364651-59365337	HepG2	liver:	n/a	n/a
3	JUND	chr1:59364701-59365140	HepG2	liver:	n/a	n/a
4	ZNF384	chr1:59364674-59365073	K562	blood:	n/a	n/a
5	MAZ	chr1:59364485-59365417	K562	blood:	n/a	n/a
6	REST	chr1:59364644-59365397	K562	blood:	n/a	n/a
7	ZNF143	chr1:59364501-59365330	K562	blood:	n/a	chr1:59364599-59364608
8	ELF1	chr1:59364651-59365056	HepG2	liver:	n/a	n/a
9	GATA2	chr1:59364657-59365015	SH-SY5Y	brain:	n/a	n/a
10	SP1	chr1:59364605-59365300	HepG2	liver:	n/a	n/a
11	MYC	chr1:59364747-59365037	K562	blood:	n/a	n/a
12	CEBPD	chr1:59364565-59365454	K562	blood:	n/a	n/a
13	YY1	chr1:59364602-59364955	HepG2	liver:	n/a	n/a
14	FOXA1	chr1:59364588-59365371	HepG2	liver:	n/a	n/a
15	MXI1	chr1:59364666-59365187	K562	blood:	n/a	n/a
16	EP300	chr1:59364657-59364939	SK-N-SH_RA	brain:	n/a	chr1:59364686-59364695
17	FOXA1	chr1:59364601-59365298	HepG2	liver:	n/a	n/a
18	E2F6	chr1:59364690-59365003	K562	blood:	n/a	n/a
19	REST	chr1:59364676-59365303	K562	blood:	n/a	n/a
20	CUX1	chr1:59364568-59365962	K562	blood:	n/a	n/a
21	ZBTB7A	chr1:59364625-59365047	K562	blood:	n/a	n/a
22	ELF1	chr1:59364558-59364994	K562	blood:	n/a	n/a
23	POLR2A	chr1:59364523-59365433	K562	blood:	n/a	n/a
24	RFX5	chr1:59364742-59365244	HepG2	liver:	n/a	n/a
25	MAX	chr1:59364595-59365492	K562	blood:	n/a	n/a
26	STAT5A	chr1:59364513-59365446	K562	blood:	n/a	n/a
27	GATA1	chr1:59364412-59365541	PBDE	blood:	n/a	n/a
28	CBX3	chr1:59364672-59365378	K562	blood:	n/a	n/a
29	CREB1	chr1:59364306-59365458	K562	blood:	n/a	n/a
30	EP300	chr1:59364272-59365334	K562	blood:	n/a	chr1:59364686-59364695
31	SPI1	chr1:59364609-59365024	K562	blood:	n/a	n/a
32	HNF4A	chr1:59364670-59365312	HepG2	liver:	n/a	chr1:59364975-59364990
33	TBL1XR1	chr1:59364578-59365747	K562	blood:	n/a	n/a
34	CCNT2	chr1:59364581-59365400	K562	blood:	n/a	n/a
35	BACH1	chr1:59364648-59364987	K562	blood:	n/a	n/a
36	TBP	chr1:59364669-59365254	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:59364592-59365274	K562	blood:	n/a	n/a
38	USF1	chr1:59364564-59365327	K562	blood:	n/a	chr1:59364863-59364874
39	RAD21	chr1:59364664-59364987	SK-N-SH_RA	brain:	n/a	n/a
40	NFIC	chr1:59364637-59365148	HepG2	liver:	n/a	n/a
41	CTCF	chr1:59364860-59365010	BE2_C	brain:	n/a	n/a
42	GATA1	chr1:59364657-59365359	K562	blood:	n/a	n/a
43	SP1	chr1:59364568-59365195	K562	blood:	n/a	n/a
44	ELF1	chr1:59364565-59365398	K562	blood:	n/a	n/a
45	JUN	chr1:59364236-59365333	K562	blood:	n/a	chr1:59364470-59364484
46	HEY1	chr1:59364669-59364935	HepG2	liver:	n/a	n/a
47	RAD21	chr1:59364674-59365138	HepG2	liver:	n/a	n/a
48	GATA1	chr1:59364678-59365235	PBDEFetal	blood:	n/a	n/a
49	GABPA	chr1:59364586-59365038	K562	blood:	n/a	n/a
50	TBL1XR1	chr1:59364613-59365494	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59335945..59337936-chr1:59364743..59367099,2	K562	blood:
2	chr1:59242448..59252747-chr1:59356992..59375072,48	K562	blood:
3	chr1:59363087..59366662-chr1:59367277..59371776,8	K562	blood:
4	chr1:59242448..59251438-chr1:59358057..59375559,39	K562	blood:
5	chr1:59364854..59367542-chr1:59372083..59374801,2	K562	blood:
6	chr1:59316456..59319340-chr1:59363706..59366262,2	K562	blood:
7	chr1:59285707..59288503-chr1:59364904..59368288,3	K562	blood:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FGGY-5	chr1:59364719-59365265	ENSG00000234807
2	lnc-FGGY-5	chr1:59364719-59365384	ENSG00000234807
3	lnc-FGGY-5	chr1:59364719-59365384	NONHSAT003524
4	lnc-FGGY-5	chr1:59364719-59365266	NONHSAT003525
5	lnc-FGGY-5	chr1:59364719-59365384	NR_108106
6	lnc-FGGY-5	chr1:59364719-59365266	ENSG00000234807.4

No data

Variant related genes	Relation type
ENSG00000232453	TF binding region
ENSG00000177606	Chromatin interaction
ENSG00000234807	Chromatin interaction
ENSG00000231740	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10493253	0.87[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10789072	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11207319	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11207321	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11207322	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11207323	0.87[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11207325	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207326	0.87[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11207332	0.82[EUR][1000 genomes]
rs12117564	0.87[CEU][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12122077	0.88[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs12142126	0.80[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12409909	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1536159	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17118379	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2057596	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2716105	0.83[JPT][hapmap]
rs2953373	0.80[EUR][1000 genomes]
rs41287666	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6587841	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6661505	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6677752	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6681632	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6697107	0.87[CEU][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7528731	0.91[CEU][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005354	chr1:59283572-59535812	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv829959	chr1:59340330-59503085	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59356200-59368600	Weak transcription	Esophagus	oesophagus
2	chr1:59358200-59367200	Enhancers	HUVEC	blood vessel
3	chr1:59358400-59368600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr1:59358600-59367000	Enhancers	Adipose Nuclei	Adipose
5	chr1:59358800-59365800	Enhancers	Lung	lung
6	chr1:59358800-59367000	Enhancers	Fetal Muscle Leg	muscle
7	chr1:59359000-59365800	Enhancers	Left Ventricle	heart
8	chr1:59359000-59366400	Enhancers	Primary hematopoietic stem cells	blood
9	chr1:59359000-59367000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:59359000-59367200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:59359000-59368600	Enhancers	Fetal Intestine Small	intestine
12	chr1:59359000-59368800	Enhancers	Fetal Intestine Large	intestine
13	chr1:59359200-59366400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:59359600-59365600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr1:59359600-59365600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:59360000-59367000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr1:59360600-59365400	Enhancers	Spleen	Spleen
18	chr1:59360600-59366600	Enhancers	Colonic Mucosa	Colon
19	chr1:59360800-59365000	Enhancers	Fetal Heart	heart
20	chr1:59360800-59365000	Enhancers	Placenta	Placenta
21	chr1:59361000-59366600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr1:59361200-59367000	Enhancers	Ovary	ovary
23	chr1:59361200-59368800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:59361600-59367000	Enhancers	Fetal Lung	lung
25	chr1:59361600-59368400	Weak transcription	GM12878-XiMat	blood
26	chr1:59361800-59368800	Weak transcription	HMEC	breast
27	chr1:59362000-59366000	Weak transcription	Osteobl	bone
28	chr1:59362200-59366600	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr1:59362400-59368600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:59362400-59368600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:59362400-59368800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:59362400-59369000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:59362600-59368600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:59362600-59368800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:59362600-59368800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:59362800-59367800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:59362800-59367800	Weak transcription	Fetal Thymus	thymus
38	chr1:59362800-59368600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:59362800-59368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:59362800-59368800	Weak transcription	NH-A	brain
41	chr1:59362800-59368800	Weak transcription	NHEK	skin
42	chr1:59362800-59369000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr1:59362800-59369000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:59363000-59365800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:59363000-59366000	Weak transcription	NHDF-Ad	bronchial
46	chr1:59363000-59366200	Weak transcription	NHLF	lung
47	chr1:59363200-59366800	Weak transcription	Hela-S3	cervix
48	chr1:59363200-59368400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr1:59363200-59368600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:59363200-59369000	Weak transcription	Brain Angular Gyrus	brain

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