Variant report

Variant	rs12531742
Chromosome Location	chr7:97651194-97651195
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	JUND	chr7:97650792-97651229	A549	lung:	n/a	n/a
2	WRNIP1	chr7:97650894-97651239	GM12878	blood:	n/a	n/a
3	RAD21	chr7:97650843-97651230	GM12878	blood:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
4	CTCF	chr7:97650753-97651349	MCF-7	breast:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
5	CCNT2	chr7:97650923-97651198	K562	blood:	n/a	n/a
6	CTCF	chr7:97650795-97651219	K562	blood:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
7	RAD21	chr7:97650573-97651637	SK-N-SH	brain:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
8	RAD21	chr7:97650676-97651490	HCT-116	colon:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
9	ZNF143	chr7:97650853-97651216	H1-hESC	embryonic stem cell:	n/a	n/a
10	RCOR1	chr7:97650922-97651198	GM12878	blood:	n/a	n/a
11	YY1	chr7:97650877-97651194	GM12878	blood:	n/a	n/a
12	ZNF143	chr7:97650860-97651383	Hela-S3	cervix:	n/a	n/a
13	EBF1	chr7:97650796-97651211	GM12878	blood:	n/a	chr7:97650974-97650985 chr7:97651007-97651018 chr7:97650976-97650985
14	RAD21	chr7:97650643-97651379	HCT-116	colon:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
15	SMC3	chr7:97650802-97651298	Hela-S3	cervix:	n/a	chr7:97651008-97651015 chr7:97651012-97651022 chr7:97651008-97651022
16	CTCF	chr7:97650748-97651265	A549	lung:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
17	MAZ	chr7:97650865-97651289	IMR90	lung:	n/a	n/a
18	RAD21	chr7:97650868-97651204	GM12878	blood:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
19	POLR2A	chr7:97651147-97651300	MCF-7	breast:	n/a	n/a
20	YY1	chr7:97650834-97651423	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZNF263	chr7:97650880-97651293	HEK293-T-REx	kidney:	n/a	chr7:97651146-97651167
22	CTCF	chr7:97650859-97651360	K562	blood:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
23	CTCF	chr7:97650722-97651396	MCF-7	breast:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
24	RAD21	chr7:97650839-97651202	K562	blood:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
25	YY1	chr7:97650881-97651236	K562	blood:	n/a	n/a
26	MAX	chr7:97650967-97651238	GM12878	blood:	n/a	n/a
27	SMC3	chr7:97650829-97651261	K562	blood:	n/a	chr7:97651008-97651015 chr7:97651012-97651022 chr7:97651008-97651022
28	RAD21	chr7:97650837-97651214	A549	lung:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
29	CTCF	chr7:97650806-97651255	IMR90	lung:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
30	RAD21	chr7:97650857-97651321	H1-hESC	embryonic stem cell:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
31	CEBPB	chr7:97650854-97651494	HepG2	liver:	n/a	n/a
32	RFX5	chr7:97650995-97651195	HepG2	liver:	n/a	n/a
33	RAD21	chr7:97650718-97651286	ECC-1	luminal epithelium:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
34	CTCF	chr7:97650862-97651229	H1-hESC	embryonic stem cell:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
35	RCOR1	chr7:97650858-97651217	K562	blood:	n/a	n/a
36	CEBPB	chr7:97650861-97651336	Hela-S3	cervix:	n/a	n/a
37	MAFF	chr7:97651070-97651215	HepG2	liver:	n/a	n/a
38	RAD21	chr7:97650708-97651347	H1-hESC	embryonic stem cell:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
39	SMC3	chr7:97650828-97651394	GM12878	blood:	n/a	chr7:97651008-97651015 chr7:97651012-97651022 chr7:97651008-97651022
40	CTCF	chr7:97650665-97651585	A549	lung:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
41	RAD21	chr7:97650761-97651407	A549	lung:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
42	RAD21	chr7:97650845-97651345	A549	lung:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
43	RAD21	chr7:97650867-97651211	K562	blood:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
44	CUX1	chr7:97650915-97651321	K562	blood:	n/a	n/a
45	CTCF	chr7:97650860-97651260	K562	blood:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
46	RAD21	chr7:97650833-97651215	SK-N-SH_RA	brain:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
47	CTCF	chr7:97650796-97651200	A549	lung:	n/a	chr7:97651009-97651022 chr7:97651007-97651023 chr7:97651008-97651029 chr7:97651009-97651018 chr7:97651009-97651022 chr7:97651011-97651021 chr7:97651006-97651024
48	RAD21	chr7:97650813-97651271	H1-hESC	embryonic stem cell:	n/a	chr7:97651010-97651023 chr7:97651012-97651022 chr7:97651007-97651026 chr7:97651012-97651024 chr7:97651008-97651022
49	HCFC1	chr7:97650929-97651235	K562	blood:	n/a	n/a
50	ZNF143	chr7:97650825-97651206	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:97650523..97652025-chr7:97797434..97798619,17	K562	blood:
2	chr7:97650843..97651448-chr7:97870469..97871701,3	MCF-7	breast:
3	chr7:97650698..97651985-chr7:97794929..97796075,7	MCF-7	breast:
4	chr7:97650523..97651440-chr7:97797679..97798686,5	MCF-7	breast:
5	chr7:97650577..97651482-chr7:97794933..97796156,10	MCF-7	breast:
6	chr7:97650988..97651925-chr7:97795533..97796074,2	K562	blood:
7	chr7:97650593..97651525-chr7:97735232..97736459,4	MCF-7	breast:
8	chr7:97651077..97652849-chr7:97796480..97798083,2	MCF-7	breast:
9	chr7:97650628..97651440-chr7:97739722..97740636,2	MCF-7	breast:
10	chr7:97650735..97651576-chr7:97797624..97798555,4	MCF-7	breast:

Variant related genes	Relation type
RN7SL13P	TF binding region
ENSG00000164715	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11974355	0.85[EUR][1000 genomes]
rs12530974	0.94[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12670761	0.84[EUR][1000 genomes]
rs12672767	0.84[EUR][1000 genomes]
rs17169244	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58823769	0.81[EUR][1000 genomes]
rs73140997	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740209	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97649200-97668000	Weak transcription	Right Atrium	heart
2	chr7:97650800-97651200	Enhancers	Fetal Muscle Trunk	muscle
3	chr7:97650800-97651400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
4	chr7:97651000-97651200	Active TSS	Brain Angular Gyrus	brain
5	chr7:97651000-97651200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr7:97651000-97651200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr7:97651000-97651200	Active TSS	Brain Substantia Nigra	brain
8	chr7:97651000-97651200	Flanking Active TSS	HepG2	liver
9	chr7:97651000-97651400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr7:97651000-97651400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
11	chr7:97651000-97651400	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr7:97651000-97651400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr7:97651000-97651400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr7:97651000-97651400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr7:97651000-97651400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr7:97651000-97651400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:97651000-97651400	Enhancers	Liver	Liver
18	chr7:97651000-97651400	Enhancers	Fetal Brain Male	brain
19	chr7:97651000-97651400	Enhancers	Pancreas	Pancrea
20	chr7:97651000-97651400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr7:97651000-97651400	Bivalent Enhancer	Stomach Mucosa	stomach
22	chr7:97651000-97651400	Enhancers	Dnd41	blood

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