Variant report

Variant	rs6699320
Chromosome Location	chr1:9887628-9887629
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:9887627-9887958	K562	blood:	n/a	n/a
2	MAX	chr1:9887546-9888043	K562	blood:	n/a	n/a
3	UBTF	chr1:9887577-9887981	K562	blood:	n/a	n/a
4	TEAD4	chr1:9887595-9888332	K562	blood:	n/a	n/a
5	ZNF384	chr1:9887293-9888240	K562	blood:	n/a	n/a
6	CTCF	chr1:9887600-9887750	GM12873	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:9883311..9885843-chr1:9886647..9889506,4	K562	blood:
2	chr1:9882501..9887964-chr1:9906388..9911794,10	MCF-7	breast:
3	chr1:9885959..9887810-chr1:9888223..9890308,2	K562	blood:
4	chr1:9886240..9887970-chr1:9893394..9897363,3	K562	blood:

No data

Variant related genes	Relation type
CLSTN1	TF binding region
ENSG00000171603	Chromatin interaction
ENSG00000223989	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10779731	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs10864436	1.00[CEU][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10864437	0.82[EUR][1000 genomes]
rs10864438	0.84[EUR][1000 genomes]
rs11121486	0.87[ASW][hapmap];0.85[CEU][hapmap];0.86[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs11121492	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11121493	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11674	0.84[EUR][1000 genomes]
rs11806520	0.87[EUR][1000 genomes]
rs12034239	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12037599	0.85[CEU][hapmap]
rs12042293	0.87[ASW][hapmap];0.85[CEU][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap]
rs12047054	1.00[CEU][hapmap];0.92[TSI][hapmap]
rs12078414	1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs12087051	0.91[EUR][1000 genomes]
rs12088273	0.82[EUR][1000 genomes]
rs1228434	0.94[EUR][1000 genomes]
rs12568720	0.85[CEU][hapmap]
rs12569008	0.85[CEU][hapmap]
rs1615629	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1631962	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1660741	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1660742	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17034335	1.00[CEU][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs17034340	0.86[EUR][1000 genomes]
rs1767277	1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2788605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs41280776	0.86[ASN][1000 genomes]
rs4585981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56109009	0.84[EUR][1000 genomes]
rs57480158	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57560942	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59729812	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72855716	0.84[EUR][1000 genomes]
rs72855733	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855735	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72855745	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72855747	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7526958	0.85[CEU][hapmap]
rs7550246	0.84[EUR][1000 genomes]
rs7550295	0.85[CEU][hapmap]
rs767762	1.00[CEU][hapmap];0.96[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs935071	0.91[EUR][1000 genomes]
rs946277	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946278	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946279	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription 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	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9885000-9888000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:9885600-9894400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:9885800-9895200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:9885800-9895600	Weak transcription	Spleen	Spleen
5	chr1:9885800-9896200	Weak transcription	Psoas Muscle	Psoas
6	chr1:9886000-9887800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:9886000-9887800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:9886000-9887800	Weak transcription	Placenta	Placenta
9	chr1:9886000-9887800	Weak transcription	Fetal Thymus	thymus
10	chr1:9886000-9891200	Weak transcription	Esophagus	oesophagus
11	chr1:9886000-9893800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:9886000-9895600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:9886000-9895600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:9886000-9895600	Weak transcription	Right Atrium	heart
15	chr1:9886200-9887800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:9886200-9887800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:9886200-9887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:9886200-9887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:9886200-9887800	Weak transcription	Osteobl	bone
20	chr1:9886200-9891200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:9886200-9895400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:9887000-9895400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:9887200-9888200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr1:9887200-9894000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:9887600-9887800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
26	chr1:9887600-9887800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:9887600-9887800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:9887600-9887800	Enhancers	HMEC	breast
29	chr1:9887600-9887800	Bivalent Enhancer	K562	blood
30	chr1:9887600-9888000	Enhancers	H1 Cell Line	embryonic stem cell
31	chr1:9887600-9888000	Flanking Bivalent TSS/Enh	HepG2	liver
32	chr1:9887600-9888200	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:9887600-9888200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:9887600-9888400	Flanking Active TSS	NHEK	skin

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