Variant report

Variant	rs10908750
Chromosome Location	chr1:159906156-159906157
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	REST	chr1:159905320-159906167	PANC-1	pancreas:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683
2	CTCF	chr1:159906023-159906548	GM12892	blood:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
3	RAD21	chr1:159906151-159906707	H1-hESC	embryonic stem cell:	n/a	chr1:159906375-159906389 chr1:159906374-159906393
4	CTCF	chr1:159906142-159906620	IMR90	lung:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
5	ZNF143	chr1:159906120-159906631	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUN	chr1:159906048-159907019	K562	blood:	n/a	n/a
7	CTCF	chr1:159906112-159906620	MCF-7	breast:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
8	TCF12	chr1:159906130-159906717	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr1:159906046-159906677	MCF-7	breast:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
10	CTCF	chr1:159906121-159906546	T-47D	breast:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
11	REST	chr1:159906086-159906479	SK-N-SH	brain:	n/a	n/a
12	RAD21	chr1:159906144-159906615	IMR90	lung:	n/a	chr1:159906375-159906389 chr1:159906374-159906393
13	REST	chr1:159906043-159906552	U87	brain:	n/a	n/a
14	RAD21	chr1:159906075-159906711	H1-hESC	embryonic stem cell:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
15	ZMIZ1	chr1:159906155-159906519	K562	blood:	n/a	n/a
16	REST	chr1:159904617-159906676	HL-60	blood:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159905104-159905114 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683
17	RAD21	chr1:159906129-159906599	SK-N-SH_RA	brain:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
18	SMC3	chr1:159906018-159906874	SK-N-SH	brain:	n/a	chr1:159906375-159906389
19	REST	chr1:159905174-159906584	ECC-1	luminal epithelium:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683
20	REST	chr1:159906121-159906570	GM12878	blood:	n/a	n/a
21	RAD21	chr1:159905827-159906851	HCT-116	colon:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
22	HMGN3	chr1:159906146-159906574	K562	blood:	n/a	n/a
23	REST	chr1:159906130-159906480	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr1:159906123-159906699	MCF-7	breast:	n/a	n/a
25	REST	chr1:159905222-159906457	A549	lung:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683
26	CTCF	chr1:159906035-159906569	GM19238	blood:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
27	REST	chr1:159905083-159906585	HL-60	blood:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159905104-159905114 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683
28	CTCF	chr1:159906047-159906721	HCT-116	colon:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
29	USF1	chr1:159906141-159906567	A549	lung:	n/a	n/a
30	REST	chr1:159906029-159906552	U87	brain:	n/a	n/a
31	CTCF	chr1:159906109-159906619	T-47D	breast:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
32	RAD21	chr1:159905888-159906787	SK-N-SH	brain:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
33	RAD21	chr1:159906144-159906671	ECC-1	luminal epithelium:	n/a	chr1:159906375-159906389 chr1:159906374-159906393
34	CTCF	chr1:159906079-159906681	K562	blood:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
35	CTCF	chr1:159906062-159906536	GM19239	blood:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
36	RAD21	chr1:159906097-159906749	H1-hESC	embryonic stem cell:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
37	RAD21	chr1:159905996-159906771	ECC-1	luminal epithelium:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
38	REST	chr1:159906093-159906462	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr1:159906053-159906705	MCF-7	breast:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
40	POLR2A	chr1:159906132-159906475	H1-hESC	embryonic stem cell:	n/a	n/a
41	RAD21	chr1:159906129-159906622	A549	lung:	n/a	chr1:159906375-159906389 chr1:159906374-159906393 chr1:159906135-159906147
42	CTCF	chr1:159905822-159907417	A549	lung:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906782-159906795 chr1:159906376-159906389
43	SMC3	chr1:159906143-159906624	K562	blood:	n/a	chr1:159906375-159906389
44	CTCF	chr1:159906028-159906575	GM12878	blood:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
45	REST	chr1:159905216-159906573	MCF-7	breast:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683
46	ZNF263	chr1:159906081-159907764	HEK293-T-REx	kidney:	n/a	chr1:159906311-159906332 chr1:159907429-159907438 chr1:159907432-159907441 chr1:159907632-159907641
47	MAZ	chr1:159906038-159906532	IMR90	lung:	n/a	n/a
48	ELF1	chr1:159906121-159906656	GM12878	blood:	n/a	n/a
49	CTCF	chr1:159906074-159906611	H1-hESC	embryonic stem cell:	n/a	chr1:159906373-159906391 chr1:159906375-159906396 chr1:159906376-159906389
50	REST	chr1:159905124-159906547	ECC-1	luminal epithelium:	n/a	chr1:159905668-159905682 chr1:159905668-159905688 chr1:159905668-159905688 chr1:159906020-159906028 chr1:159905668-159905688 chr1:159905674-159905683

No.	Distal block	Cell Line	Cell type
1	chr1:159905976..159906804-chr1:159915105..159915809,2	K562	blood:
2	chr1:159905804..159907372-chr1:159975809..159978372,14	K562	blood:
3	chr1:159906056..159906677-chr1:159975139..159975691,2	K562	blood:
4	chr1:159899215..159903293-chr1:159903611..159908278,6	MCF-7	breast:
5	chr1:159905881..159908106-chr1:159914629..159916330,2	K562	blood:
6	chr1:159905858..159907712-chr1:159975951..159977726,16	MCF-7	breast:
7	chr1:159905137..159907886-chr1:159939775..159941971,2	MCF-7	breast:
8	chr1:159861441..159862059-chr1:159905937..159906869,2	MCF-7	breast:
9	chr1:159905870..159907059-chr1:159974065..159975500,4	MCF-7	breast:
10	chr1:159905575..159906818-chr1:159976875..159978062,9	MCF-7	breast:
11	chr1:159905895..159906869-chr1:160048168..160049061,2	K562	blood:
12	chr1:159905321..159906863-chr1:159975858..159976873,27	MCF-7	breast:
13	chr1:159906023..159906836-chr1:160048195..160048850,3	MCF-7	breast:

Variant related genes	Relation type
IGSF9	TF binding region
ENSG00000085552	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10752634	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797054	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10797055	0.94[ASN][1000 genomes]
rs12139175	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1320566	0.89[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1934074	0.81[CEU][hapmap]
rs1934075	0.81[CEU][hapmap];0.87[MEX][hapmap];0.85[AMR][1000 genomes]
rs6658042	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6703466	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7524321	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526647	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv872489	chr1:159844819-159940000	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv464150	chr1:159860917-159908393	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv548052	chr1:159860917-159908393	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv548053	chr1:159885500-159908393	Flanking Bivalent TSS/Enh Genic enhancers Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
6	nsv524006	chr1:159886422-159923111	Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv516637	chr1:159889686-159908393	Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	62 gene(s)	inside rSNPs	diseases
8	nsv548054	chr1:159895979-159907441	Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159895800-159906600	Weak transcription	Small Intestine	intestine
2	chr1:159896400-159906600	Weak transcription	Right Atrium	heart
3	chr1:159896600-159907200	Weak transcription	Fetal Heart	heart
4	chr1:159896600-159908600	Weak transcription	Fetal Kidney	kidney
5	chr1:159897000-159906200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:159897000-159906200	Strong transcription	Fetal Brain Female	brain
7	chr1:159897800-159906400	Weak transcription	Fetal Brain Male	brain
8	chr1:159899400-159906200	Weak transcription	Gastric	stomach
9	chr1:159899400-159906400	Strong transcription	Fetal Stomach	stomach
10	chr1:159900000-159906400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:159902800-159906400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:159902800-159906400	Weak transcription	Fetal Lung	lung
13	chr1:159903000-159906200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:159903200-159906600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:159903600-159908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:159903800-159906600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:159904000-159906400	Strong transcription	NHEK	skin
18	chr1:159904600-159906400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:159905000-159906600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:159905400-159907200	Enhancers	Stomach Mucosa	stomach
21	chr1:159905400-159908400	Enhancers	Primary B cells from cord blood	blood
22	chr1:159905400-159908600	Enhancers	Primary B cells from peripheral blood	blood
23	chr1:159905400-159909600	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:159905400-159909800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:159905600-159906200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:159905600-159906200	Genic enhancers	Fetal Intestine Large	intestine
27	chr1:159905600-159906600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:159905600-159906800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:159905600-159907000	Enhancers	GM12878-XiMat	blood
30	chr1:159905600-159907200	Enhancers	Hela-S3	cervix
31	chr1:159905600-159908400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr1:159905800-159906200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:159905800-159906200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:159905800-159906400	Enhancers	Brain Substantia Nigra	brain
35	chr1:159905800-159906600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:159905800-159906800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:159905800-159906800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:159905800-159907400	Enhancers	A549	lung
39	chr1:159905800-159908200	Enhancers	Primary hematopoietic stem cells	blood
40	chr1:159905800-159908200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:159905800-159908400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:159905800-159908600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr1:159905800-159908600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr1:159905800-159911400	Enhancers	Placenta	Placenta
45	chr1:159905800-159913600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:159906000-159906200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:159906000-159906200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:159906000-159906200	Genic enhancers	Colonic Mucosa	Colon
49	chr1:159906000-159906200	Enhancers	Rectal Smooth Muscle	rectum
50	chr1:159906000-159906200	Bivalent Enhancer	Stomach Smooth Muscle	stomach

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