Variant report

Variant	rs10743660
Chromosome Location	chr12:9472015-9472016
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	CTCF	chr12:9471940-9472090	GM12872	blood:	n/a	chr12:9472004-9472017
2	CTCF	chr12:9471912-9472099	K562	blood:	n/a	chr12:9472004-9472017
3	RAD21	chr12:9471821-9472133	HepG2	liver:	n/a	chr12:9472057-9472070
4	RAD21	chr12:9471887-9472055	SK-N-SH_RA	brain:	n/a	n/a
5	CTCF	chr12:9471940-9472118	GM13977	blood:	n/a	chr12:9472004-9472017
6	PAX5	chr12:9471961-9472856	GM12878	blood:	n/a	n/a
7	CTCF	chr12:9471894-9472090	A549	lung:	n/a	chr12:9472004-9472017
8	RAD21	chr12:9471757-9472133	HepG2	liver:	n/a	chr12:9472057-9472070
9	CTCF	chr12:9471920-9472070	HA-sp	spinal cord:	n/a	chr12:9472004-9472017
10	POLR2A	chr12:9471684-9472079	HepG2	liver:	n/a	n/a
11	CTCF	chr12:9471880-9472030	HVMF	connective:	n/a	chr12:9472004-9472017
12	CTCF	chr12:9471900-9472050	HCPEpiC	choroid plexus:	n/a	chr12:9472004-9472017
13	CTCF	chr12:9471906-9472118	Gliobla	brain:	n/a	chr12:9472004-9472017
14	CTCF	chr12:9471934-9472115	LNCaP	prostate:	n/a	chr12:9472004-9472017
15	POU2F2	chr12:9471897-9472550	GM12891	blood:	n/a	chr12:9472366-9472373
16	CTCF	chr12:9471933-9472096	NHEK	skin:	n/a	chr12:9472004-9472017
17	CTCF	chr12:9471950-9472085	HepG2	liver:	n/a	chr12:9472004-9472017
18	CTCF	chr12:9471900-9472050	MCF-7	breast:	n/a	chr12:9472004-9472017
19	CTCF	chr12:9471900-9472050	HUVEC	blood vessel:	n/a	chr12:9472004-9472017
20	RAD21	chr12:9471806-9472093	MCF-7	breast:	n/a	chr12:9472057-9472070
21	CTCF	chr12:9471923-9472117	MCF-7	breast:	n/a	chr12:9472004-9472017
22	CTCF	chr12:9471940-9472090	GM12865	blood:	n/a	chr12:9472004-9472017
23	CTCF	chr12:9471897-9472134	MCF-7	breast:	n/a	chr12:9472004-9472017
24	CTCF	chr12:9471969-9472101	A549	lung:	n/a	chr12:9472004-9472017
25	CTCF	chr12:9471900-9472050	HEK293	kidney:	n/a	chr12:9472004-9472017
26	RAD21	chr12:9471802-9472087	ECC-1	luminal epithelium:	n/a	chr12:9472057-9472070
27	CTCF	chr12:9471880-9472030	GM12865	blood:	n/a	chr12:9472004-9472017
28	CTCF	chr12:9471779-9472118	MCF-7	breast:	n/a	chr12:9472004-9472017
29	CTCF	chr12:9471920-9472070	GM12866	blood:	n/a	chr12:9472004-9472017
30	CTCF	chr12:9472000-9472150	GM12878	blood:	n/a	chr12:9472004-9472017
31	CTCF	chr12:9471900-9472050	SK-N-SH_RA	brain:	n/a	chr12:9472004-9472017
32	CTCF	chr12:9471941-9472050	SK-N-SH_RA	brain:	n/a	chr12:9472004-9472017
33	CTCF	chr12:9471880-9472030	RPTEC	kidney:	n/a	chr12:9472004-9472017
34	CTCF	chr12:9471920-9472070	HepG2	liver:	n/a	chr12:9472004-9472017
35	CTCF	chr12:9471942-9472106	Medullo	brain:	n/a	chr12:9472004-9472017
36	CTCF	chr12:9471880-9472030	HRPEpiC	eye:	n/a	chr12:9472004-9472017
37	CTCF	chr12:9471940-9472090	GM12870	blood:	n/a	chr12:9472004-9472017
38	CTCF	chr12:9471900-9472050	Caco-2	colon:	n/a	chr12:9472004-9472017
39	CTCF	chr12:9472000-9472150	Hela-S3	cervix:	n/a	chr12:9472004-9472017
40	CTCF	chr12:9471916-9472119	MCF-7	breast:	n/a	chr12:9472004-9472017
41	CTCF	chr12:9471920-9472070	BJ	skin:	n/a	chr12:9472004-9472017
42	CTCF	chr12:9471880-9472030	MCF-7	breast:	n/a	chr12:9472004-9472017
43	CTCF	chr12:9471880-9472030	WI-38	lung:	n/a	chr12:9472004-9472017
44	CTCF	chr12:9471976-9472070	Lung_OC	lung:	n/a	chr12:9472004-9472017
45	RAD21	chr12:9471838-9472105	H1-hESC	embryonic stem cell:	n/a	chr12:9472057-9472070
46	CTCF	chr12:9471920-9472070	HPF	lung:	n/a	chr12:9472004-9472017
47	CTCF	chr12:9471900-9472050	GM12873	blood:	n/a	chr12:9472004-9472017
48	CTCF	chr12:9471900-9472050	GM12864	blood:	n/a	chr12:9472004-9472017
49	CTCF	chr12:9471900-9472050	BJ	skin:	n/a	chr12:9472004-9472017
50	CTCF	chr12:9471926-9472108	MCF-7	breast:	n/a	chr12:9472004-9472017

No.	Distal block	Cell Line	Cell type
1	chr12:9216104..9218306-chr12:9470179..9473467,3	MCF-7	breast:
2	chr12:9471846..9472542-chr12:9564639..9565202,2	MCF-7	breast:
3	chr12:9215714..9219195-chr12:9470456..9473261,3	MCF-7	breast:
4	chr12:9471764..9473665-chr12:9564371..9566160,2	MCF-7	breast:
5	chr12:9216487..9217272-chr12:9471486..9472478,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255753	TF binding region
ENSG00000245105	Chromatin interaction
ENSG00000214851	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1059171	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1059172	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10743661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771524	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771531	0.91[ASN][1000 genomes]
rs10771532	0.81[ASN][1000 genomes]
rs10843400	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10843404	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843408	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843418	0.87[ASN][1000 genomes]
rs12303026	0.82[ASN][1000 genomes]
rs2377762	0.81[ASN][1000 genomes]
rs4271437	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4589351	0.92[ASN][1000 genomes]
rs4883237	0.86[ASN][1000 genomes]
rs4883238	0.82[ASN][1000 genomes]
rs6487824	0.86[ASN][1000 genomes]
rs7299515	0.84[ASN][1000 genomes]
rs7311758	0.83[ASN][1000 genomes]
rs7954383	0.91[ASN][1000 genomes]
rs7957287	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv976566	chr12:9469779-9481646	Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10743660	RP11-22B23.1	cis	lung	GTEx
rs10743660	RP11-22B23.1	cis	Heart Left Ventricle	GTEx
rs10743660	DDX12P	cis	Artery Tibial	GTEx
rs10743660	RP11-22B23.1	cis	Artery Tibial	GTEx
rs10743660	RP13-735L24.1	cis	Muscle Skeletal	GTEx
rs10743660	RP11-22B23.1	cis	Whole Blood	GTEx
rs10743660	RP11-22B23.1	cis	Esophagus Muscularis	GTEx
rs10743660	DDX12P	cis	Muscle Skeletal	GTEx
rs10743660	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs10743660	RP11-22B23.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10743660	RP11-22B23.1	cis	Artery Aorta	GTEx
rs10743660	RP11-22B23.1	cis	Thyroid	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9437200-9472400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr12:9437200-9485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9456200-9472200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:9457400-9485800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr12:9458000-9472200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:9463000-9479000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:9464400-9477600	Weak transcription	Lung	lung
8	chr12:9464600-9487600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:9464800-9472200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr12:9464800-9472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:9464800-9490000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:9465000-9472600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:9465000-9473000	Weak transcription	Esophagus	oesophagus
14	chr12:9465000-9486400	Weak transcription	A549	lung
15	chr12:9465400-9485200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:9465600-9472200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:9465600-9477800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:9465600-9484000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:9465600-9488000	Weak transcription	Dnd41	blood
20	chr12:9466000-9484000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:9466200-9472400	Weak transcription	HMEC	breast
22	chr12:9466200-9484000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:9466400-9477400	Weak transcription	Fetal Lung	lung
24	chr12:9466400-9485200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:9466400-9487200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:9466400-9487600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:9470000-9472800	Enhancers	HepG2	liver
28	chr12:9470800-9472400	Enhancers	Brain Germinal Matrix	brain
29	chr12:9471600-9472200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:9471600-9473000	Enhancers	Fetal Thymus	thymus
31	chr12:9471600-9473400	Enhancers	Primary B cells from peripheral blood	blood
32	chr12:9471800-9472600	Weak transcription	Primary T cells from cord blood	blood
33	chr12:9471800-9472800	Enhancers	Thymus	Thymus
34	chr12:9471800-9473000	Enhancers	Primary B cells from cord blood	blood
35	chr12:9471800-9473000	Enhancers	GM12878-XiMat	blood
36	chr12:9472000-9472600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:9472000-9472600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr12:9472000-9472600	Enhancers	Colon Smooth Muscle	Colon
39	chr12:9472000-9473000	Enhancers	Fetal Kidney	kidney
40	chr12:9472000-9473200	Enhancers	Stomach Mucosa	stomach
41	chr12:9472000-9473200	Enhancers	NHEK	skin

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