Variant report

Variant	rs10761371
Chromosome Location	chr9:97806965-97806966
allele	C/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	chr9:97806601-97808755	A549	lung:	n/a	n/a
2	EP300	chr9:97806767-97808285	A549	lung:	n/a	n/a
3	SP1	chr9:97806901-97807778	A549	lung:	n/a	n/a
4	FOSL2	chr9:97806948-97807860	A549	lung:	n/a	n/a
5	POLR2A	chr9:97806952-97807769	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr9:97806933-97807902	A549	lung:	n/a	n/a
7	JUND	chr9:97806830-97807858	A549	lung:	n/a	n/a
8	TCF12	chr9:97806630-97809069	A549	lung:	n/a	chr9:97807931-97807941 chr9:97807799-97807806 chr9:97807952-97807959 chr9:97806906-97806914
9	ATF3	chr9:97806811-97808484	A549	lung:	n/a	n/a
10	BCL3	chr9:97805869-97809192	A549	lung:	n/a	chr9:97807640-97807649
11	POLR2A	chr9:97806754-97807970	A549	lung:	n/a	n/a
12	POLR2A	chr9:97806684-97807769	HepG2	liver:	n/a	n/a
13	POLR2A	chr9:97806627-97808676	A549	lung:	n/a	n/a
14	FOXA2	chr9:97806965-97807910	A549	lung:	n/a	n/a
15	MAX	chr9:97806741-97807803	A549	lung:	n/a	n/a
16	POLR2A	chr9:97806868-97807135	A549	lung:	n/a	n/a
17	CTCF	chr9:97806804-97809298	A549	lung:	n/a	chr9:97808280-97808298 chr9:97807606-97807619 chr9:97807066-97807075 chr9:97807801-97807814 chr9:97807525-97807538
18	BCL3	chr9:97806825-97808589	A549	lung:	n/a	chr9:97807640-97807649
19	CEBPB	chr9:97806948-97807706	A549	lung:	n/a	chr9:97807199-97807216
20	NR3C1	chr9:97806950-97807618	A549	lung:	n/a	n/a
21	POLR2A	chr9:97806834-97807872	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr9:97806753-97807120	MCF-7	breast:	n/a	n/a
23	GATA3	chr9:97806950-97808848	A549	lung:	n/a	chr9:97808744-97808760 chr9:97807485-97807495 chr9:97808749-97808756 chr9:97808749-97808756 chr9:97808749-97808756 chr9:97808471-97808481 chr9:97808470-97808482 chr9:97808742-97808763
24	FOXA2	chr9:97806882-97807363	A549	lung:	n/a	n/a
25	POLR2A	chr9:97806891-97807991	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:97805704..97807873-chr9:97845688..97847934,2	MCF-7	breast:
2	chr9:97680454..97683100-chr9:97804978..97806982,2	MCF-7	breast:
3	chr9:97805422..97807754-chr9:97822770..97825763,2	MCF-7	breast:
4	chr9:97799418..97802536-chr9:97804091..97807017,3	MCF-7	breast:
5	chr9:97803206..97809214-chr9:97809347..97813672,8	MCF-7	breast:
6	chr9:97763979..97769403-chr9:97805439..97812937,10	MCF-7	breast:
7	chr9:97802158..97803981-chr9:97806425..97808316,2	K562	blood:
8	chr9:97805980..97807545-chr9:97820488..97822005,2	MCF-7	breast:
9	chr9:97804181..97807973-chr9:97809683..97813710,4	K562	blood:
10	chr9:97806251..97809142-chr9:97810861..97813740,3	MCF-7	breast:

Variant related genes	Relation type
C9orf3	TF binding region
ENSG00000148120	Chromatin interaction
ENSG00000207563	Chromatin interaction
ENSG00000207864	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1020962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217441	1.00[CEU][hapmap]
rs1038092	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732407	1.00[CEU][hapmap]
rs10761362	1.00[CEU][hapmap]
rs10993471	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12553869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12555128	1.00[JPT][hapmap]
rs12555829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1542108	1.00[CEU][hapmap]
rs1564235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571897	0.83[AMR][1000 genomes]
rs16911834	1.00[JPT][hapmap]
rs16911856	1.00[JPT][hapmap]
rs1699499	0.86[EUR][1000 genomes]
rs1871220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888945	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1888946	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061799	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2061801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104888	1.00[JPT][hapmap]
rs2306207	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs242448	1.00[JPT][hapmap]
rs356660	1.00[JPT][hapmap]
rs356661	1.00[JPT][hapmap]
rs356685	1.00[JPT][hapmap]
rs356686	1.00[JPT][hapmap]
rs3739748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap]
rs4743972	1.00[CEU][hapmap]
rs4743975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743976	0.83[AMR][1000 genomes]
rs4743977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743978	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743989	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4744421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744429	0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4744437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs475413	1.00[JPT][hapmap]
rs6479578	1.00[CEU][hapmap]
rs6479589	0.83[AMR][1000 genomes]
rs6479593	0.86[AMR][1000 genomes]
rs6479596	1.00[EUR][1000 genomes]
rs6479597	1.00[EUR][1000 genomes]
rs67134693	0.96[ASN][1000 genomes]
rs7019602	1.00[CEU][hapmap]
rs7022739	0.83[AMR][1000 genomes]
rs7022963	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap]
rs7039768	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs72750335	0.96[ASN][1000 genomes]
rs72750346	0.96[ASN][1000 genomes]
rs72750351	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750359	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72750367	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72750373	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73540087	1.00[ASN][1000 genomes]
rs7867856	1.00[CEU][hapmap]
rs894426	1.00[CEU][hapmap]
rs9299427	0.83[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	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases
2	nsv1038106	chr9:97793038-97881416	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
3	nsv1038523	chr9:97797032-97923774	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases
4	nsv540175	chr9:97797032-97923774	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	274 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97770800-97810000	Weak transcription	Primary T cells from cord blood	blood
2	chr9:97793400-97810400	Weak transcription	HUVEC	blood vessel
3	chr9:97794200-97807000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:97795000-97810400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr9:97795600-97808600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:97797000-97807800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:97798200-97808600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr9:97799400-97807600	Weak transcription	Thymus	Thymus
9	chr9:97799400-97810000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:97800000-97808600	Genic enhancers	Liver	Liver
11	chr9:97801400-97807000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr9:97801600-97810000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr9:97801800-97807000	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:97802200-97807600	Strong transcription	HSMM	muscle
15	chr9:97802400-97807200	Strong transcription	HSMMtube	muscle
16	chr9:97803000-97810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr9:97803400-97807600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:97804000-97807200	Enhancers	Pancreas	Pancrea
19	chr9:97804000-97808800	Weak transcription	Fetal Kidney	kidney
20	chr9:97804000-97810400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:97804200-97807000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr9:97804200-97807000	Weak transcription	Colonic Mucosa	Colon
23	chr9:97804200-97807800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr9:97804400-97810400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:97804400-97810800	Weak transcription	K562	blood
26	chr9:97804600-97807000	Enhancers	Fetal Heart	heart
27	chr9:97804600-97807200	Genic enhancers	HepG2	liver
28	chr9:97804800-97808200	Strong transcription	NH-A	brain
29	chr9:97804800-97808200	Strong transcription	NHLF	lung
30	chr9:97805000-97810000	Weak transcription	Brain Anterior Caudate	brain
31	chr9:97805200-97807200	Strong transcription	Hela-S3	cervix
32	chr9:97805200-97808400	Genic enhancers	Fetal Intestine Small	intestine
33	chr9:97805200-97810400	Weak transcription	Brain Angular Gyrus	brain
34	chr9:97805400-97807000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:97805400-97807200	Weak transcription	Aorta	Aorta
36	chr9:97805400-97810600	Weak transcription	Small Intestine	intestine
37	chr9:97805600-97810800	Weak transcription	GM12878-XiMat	blood
38	chr9:97805800-97807000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:97805800-97807000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:97806000-97807000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr9:97806000-97807000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:97806000-97807000	Genic enhancers	Fetal Muscle Leg	muscle
43	chr9:97806000-97807400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:97806000-97807400	Genic enhancers	Brain Substantia Nigra	brain
45	chr9:97806000-97807400	Genic enhancers	Fetal Lung	lung
46	chr9:97806000-97807600	Genic enhancers	Brain Hippocampus Middle	brain
47	chr9:97806000-97807600	Genic enhancers	Lung	lung
48	chr9:97806000-97807800	Strong transcription	Adipose Nuclei	Adipose
49	chr9:97806000-97808000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:97806000-97808000	Enhancers	Right Atrium	heart

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