Variant report

Variant	rs10509684
Chromosome Location	chr10:97003001-97003002
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	CTCF	chr10:97002880-97003030	GM12871	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
2	CTCF	chr10:97002805-97003226	K562	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
3	CTCF	chr10:97002815-97003081	HepG2	liver:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
4	CTCF	chr10:97002900-97003050	WI-38	lung:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
5	ZNF384	chr10:97002886-97003086	K562	blood:	n/a	chr10:97002988-97002996
6	RAD21	chr10:97002786-97003072	HepG2	liver:	n/a	chr10:97002964-97002983
7	CTCF	chr10:97002900-97003050	AG09309	skin:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
8	CTCF	chr10:97002880-97003030	GM12864	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
9	CTCF	chr10:97002900-97003050	AoAF	blood vessel:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
10	CTCF	chr10:97002920-97003070	MCF-7	breast:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
11	CTCF	chr10:97002940-97003090	HFF	foreskin:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
12	CTCF	chr10:97002860-97003010	NHDF-neo	bronchial:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
13	CTCF	chr10:97002880-97003030	HMEC	breast:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
14	CTCF	chr10:97002879-97003054	GM19239	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
15	RAD21	chr10:97002883-97003006	K562	blood:	n/a	chr10:97002964-97002983
16	CTCF	chr10:97002760-97003158	K562	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
17	CTCF	chr10:97002868-97003083	HepG2	liver:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
18	CTCF	chr10:97002857-97003066	Fibrobl	skin:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
19	SMC3	chr10:97002829-97003055	K562	blood:	n/a	n/a
20	CTCF	chr10:97002770-97003158	GM12878	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
21	CTCF	chr10:97002452-97003587	A549	lung:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984 chr10:97003275-97003284
22	CTCF	chr10:97002920-97003070	GM12867	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
23	RAD21	chr10:97002757-97003149	HepG2	liver:	n/a	chr10:97002964-97002983
24	CTCF	chr10:97002920-97003070	HVMF	connective:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
25	CTCF	chr10:97002710-97003247	MCF-7	breast:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
26	CTCF	chr10:97002867-97003089	Spleen_OC	spleen:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
27	CTCF	chr10:97002905-97003087	Lung_OC	lung:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
28	RAD21	chr10:97002744-97003182	IMR90	lung:	n/a	chr10:97002964-97002983
29	CTCF	chr10:97002860-97003010	A549	lung:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
30	CTCF	chr10:97002980-97003130	HCM	heart:	n/a	n/a
31	CTCF	chr10:97002920-97003070	HRPEpiC	eye:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
32	RAD21	chr10:97002610-97003188	HepG2	liver:	n/a	chr10:97002964-97002983
33	CTCF	chr10:97002875-97003080	Kidney_OC	kidney:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
34	CTCF	chr10:97002900-97003050	AG09319	gingival:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
35	CTCF	chr10:97002920-97003070	AG04450	lung:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
36	RAD21	chr10:97002813-97003026	K562	blood:	n/a	chr10:97002964-97002983
37	CTCF	chr10:97002795-97003144	K562	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
38	CTCF	chr10:97002880-97003030	AG09309	skin:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
39	CTCF	chr10:97002872-97003076	GM13977	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
40	CTCF	chr10:97002848-97003065	MCF-7	breast:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
41	CTCF	chr10:97002860-97003010	NHEK	skin:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
42	CTCF	chr10:97002920-97003070	AoAF	blood vessel:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
43	CTCF	chr10:97002860-97003096	GM12878	blood:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
44	RAD21	chr10:97002770-97003026	GM12878	blood:	n/a	chr10:97002964-97002983
45	CTCF	chr10:97002980-97003130	GM06990	blood:	n/a	n/a
46	CTCF	chr10:97002900-97003050	HCT-116	colon:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
47	CTCF	chr10:97002900-97003050	HA-sp	spinal cord:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
48	CTCF	chr10:97002880-97003030	HAc	cerebellar:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
49	CTCF	chr10:97002843-97003103	MCF-7	breast:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984
50	CTCF	chr10:97002857-97003060	MCF-7	breast:	n/a	chr10:97002967-97002983 chr10:97002961-97002982 chr10:97002966-97002984

No.	Distal block	Cell Line	Cell type
1	chr10:97002945..97004630-chr10:97004800..97006467,2	K562	blood:
2	chr10:97002381..97008883-chr10:97045266..97052392,13	MCF-7	breast:
3	chr10:96942807..96943976-chr10:97002556..97003412,6	MCF-7	breast:
4	chr10:96961108..96962057-chr10:97002638..97003736,3	MCF-7	breast:
5	chr10:96943022..96944126-chr10:97002378..97003591,25	MCF-7	breast:
6	chr10:96968177..96969122-chr10:97002506..97003338,4	MCF-7	breast:
7	chr10:97001343..97004286-chr10:97048422..97051252,2	K562	blood:

Variant related genes	Relation type
PDLIM1	TF binding region
ENSG00000107438	Chromatin interaction
ENSG00000225533	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11572127	1.00[JPT][hapmap]
rs2901832	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34386561	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34442634	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35449044	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45619340	0.84[ASN][1000 genomes]
rs623544	0.83[TSI][hapmap]
rs682349	0.83[TSI][hapmap]
rs684203	0.83[TSI][hapmap]

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	nsv497859	chr10:96058024-97027747	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv15160	chr10:96942869-97074756	Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10509684	CCNJ	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:96990800-97005200	Weak transcription	Psoas Muscle	Psoas
2	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:96991000-97006400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:96991000-97006600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr10:96991000-97006600	Weak transcription	Colon Smooth Muscle	Colon
6	chr10:96991000-97006600	Weak transcription	Right Atrium	heart
7	chr10:96991000-97007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:96991000-97020400	Weak transcription	Fetal Muscle Leg	muscle
9	chr10:96991000-97024000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr10:96991400-97019000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr10:96992000-97005000	Strong transcription	Duodenum Mucosa	Duodenum
12	chr10:96992000-97005800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:96992200-97009000	Strong transcription	Liver	Liver
14	chr10:96992400-97006200	Strong transcription	Placenta Amnion	Placenta Amnion
15	chr10:96992600-97004000	Strong transcription	Fetal Intestine Large	intestine
16	chr10:96996200-97004000	Strong transcription	Fetal Intestine Small	intestine
17	chr10:96996200-97006600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr10:96996400-97016000	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr10:96996600-97007000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr10:96996800-97005000	Strong transcription	Primary B cells from peripheral blood	blood
21	chr10:96996800-97006600	Weak transcription	HUVEC	blood vessel
22	chr10:96996800-97009400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr10:96997600-97004800	Weak transcription	NH-A	brain
24	chr10:96997600-97006200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr10:96998000-97005800	Weak transcription	Hela-S3	cervix
26	chr10:96998000-97006400	Weak transcription	NHDF-Ad	bronchial
27	chr10:96998200-97005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr10:96998200-97009400	Weak transcription	Small Intestine	intestine
29	chr10:96998400-97003200	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr10:96998400-97006200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr10:96998400-97006400	Weak transcription	HSMM	muscle
32	chr10:96998400-97006600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr10:96998400-97030200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:96999600-97008600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr10:96999800-97006600	Strong transcription	Adipose Nuclei	Adipose
36	chr10:96999800-97009000	Strong transcription	Primary B cells from cord blood	blood
37	chr10:97000000-97005600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr10:97000000-97006400	Strong transcription	NHEK	skin
39	chr10:97000000-97006600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr10:97000000-97006800	Strong transcription	Gastric	stomach
41	chr10:97000000-97009400	Strong transcription	Colonic Mucosa	Colon
42	chr10:97000200-97003200	Strong transcription	GM12878-XiMat	blood
43	chr10:97000200-97003800	Strong transcription	Placenta	Placenta
44	chr10:97000200-97006600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:97000400-97006600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr10:97000400-97006600	Strong transcription	HepG2	liver
47	chr10:97000400-97024400	Weak transcription	Fetal Kidney	kidney
48	chr10:97000600-97004800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr10:97000600-97005200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr10:97001200-97003400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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