Variant report

Variant	rs12612694
Chromosome Location	chr2:97540562-97540563
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	SP1	chr2:97540098-97540723	GM12878	blood:	n/a	n/a
2	CHD2	chr2:97539396-97540712	GM12878	blood:	n/a	n/a
3	CUX1	chr2:97539889-97540691	GM12878	blood:	n/a	n/a
4	POLR2A	chr2:97539812-97540887	GM12892	blood:	n/a	n/a
5	MTA3	chr2:97539895-97540800	GM12878	blood:	n/a	n/a
6	EBF1	chr2:97539409-97540780	GM12878	blood:	n/a	chr2:97539963-97539973 chr2:97539962-97539973 chr2:97539963-97539972
7	FOXM1	chr2:97540067-97540716	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:97539653-97541196	GM12892	blood:	n/a	n/a
9	PAX5	chr2:97539965-97540799	GM12878	blood:	n/a	chr2:97540514-97540523 chr2:97540313-97540323 chr2:97540057-97540066
10	POLR2A	chr2:97539844-97540827	GM12878	blood:	n/a	n/a
11	RUNX3	chr2:97539920-97540736	GM12878	blood:	n/a	n/a
12	EBF1	chr2:97539225-97540757	GM12878	blood:	n/a	chr2:97539963-97539973 chr2:97539962-97539973 chr2:97539963-97539972
13	PML	chr2:97539786-97540709	GM12878	blood:	n/a	n/a
14	RELA	chr2:97540060-97540634	GM10847	blood:	n/a	n/a
15	POLR2A	chr2:97539982-97540662	GM12878	blood:	n/a	n/a
16	BHLHE40	chr2:97539920-97540814	GM12878	blood:	n/a	n/a
17	PAX5	chr2:97540306-97540653	GM12878	blood:	n/a	chr2:97540514-97540523 chr2:97540313-97540323
18	POLR2A	chr2:97539897-97540670	GM12892	blood:	n/a	n/a
19	RUNX3	chr2:97540172-97540614	GM12878	blood:	n/a	n/a
20	BCLAF1	chr2:97540146-97540641	GM12878	blood:	n/a	n/a
21	RELA	chr2:97539442-97540710	GM19099	blood:	n/a	n/a
22	SP1	chr2:97540086-97540624	GM12878	blood:	n/a	n/a
23	NFATC1	chr2:97540073-97540723	GM12878	blood:	n/a	n/a
24	POU2F2	chr2:97539939-97540789	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:97540279-97540618	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:97539243-97541503	GM12878	blood:	n/a	n/a
27	POLR2A	chr2:97540365-97540568	MCF-7	breast:	n/a	n/a
28	RELA	chr2:97539872-97540740	GM18951	blood:	n/a	n/a
29	RELA	chr2:97539913-97540568	GM19193	blood:	n/a	n/a
30	BCLAF1	chr2:97539996-97540614	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:97540505-97543091	K562	blood:	n/a	n/a
32	POLR2A	chr2:97539277-97543077	K562	blood:	n/a	n/a
33	POLR2A	chr2:97537838-97552897	K562	blood:	n/a	n/a
34	POLR2A	chr2:97539500-97541285	GM12878	blood:	n/a	n/a
35	BCL3	chr2:97540119-97540644	GM12878	blood:	n/a	n/a
36	RELA	chr2:97539775-97540653	GM18505	blood:	n/a	n/a
37	USF1	chr2:97540390-97540643	GM12878	blood:	n/a	n/a
38	ELF1	chr2:97539294-97540740	GM12878	blood:	n/a	n/a
39	IRF4	chr2:97540212-97540691	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:97538088-97552551	K562	blood:	n/a	n/a
41	POLR2A	chr2:97538469-97541757	MCF10A-Er-Src	breast:	n/a	n/a
42	RELA	chr2:97540072-97540648	GM12892	blood:	n/a	n/a
43	ATF2	chr2:97539921-97540568	GM12878	blood:	n/a	n/a
44	POLR2A	chr2:97540143-97540565	GM12892	blood:	n/a	n/a
45	POLR2A	chr2:97540196-97540767	GM12892	blood:	n/a	n/a
46	SPI1	chr2:97540073-97540694	GM12891	blood:	n/a	chr2:97540264-97540273 chr2:97540265-97540272 chr2:97540263-97540276 chr2:97540262-97540275
47	MAX	chr2:97539965-97540656	GM12878	blood:	n/a	n/a
48	ZNF143	chr2:97540080-97540603	GM12878	blood:	n/a	n/a
49	RCOR1	chr2:97539442-97540826	GM12878	blood:	n/a	n/a
50	EP300	chr2:97539381-97540828	GM12878	blood:	n/a	chr2:97539547-97539561 chr2:97540264-97540273

No.	Distal block	Cell Line	Cell type
1	chr2:97516728..97547486-chr2:97588377..97628331,265	MCF-7	breast:
2	chr2:97536575..97540877-chr2:97558007..97561072,4	K562	blood:
3	chr2:97540516..97542905-chr2:97593439..97596324,2	K562	blood:
4	chr2:97516134..97518414-chr2:97539957..97542072,2	K562	blood:
5	chr2:97539206..97540823-chr2:97583681..97585433,2	K562	blood:
6	chr2:97538577..97540759-chr2:97582330..97584381,2	K562	blood:

Variant related genes	Relation type
SEMA4C	TF binding region
ENSG00000252845	Chromatin interaction
ENSG00000168754	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12615663	1.00[EUR][1000 genomes]
rs12616466	1.00[EUR][1000 genomes]
rs12620989	1.00[EUR][1000 genomes]
rs13419720	1.00[EUR][1000 genomes]
rs13421281	1.00[EUR][1000 genomes]
rs13422315	1.00[EUR][1000 genomes]
rs4481029	1.00[EUR][1000 genomes]
rs4907247	1.00[EUR][1000 genomes]
rs73959418	1.00[EUR][1000 genomes]
rs7597736	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription 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	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97536600-97541600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr2:97536800-97542000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:97536800-97546200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr2:97536800-97551800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:97536800-97555200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:97537000-97540800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:97537000-97540800	Weak transcription	Fetal Brain Male	brain
8	chr2:97537000-97541000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:97537000-97542200	Enhancers	Placenta	Placenta
10	chr2:97537200-97540600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:97537200-97540800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:97537200-97540800	Weak transcription	Fetal Brain Female	brain
13	chr2:97537400-97540600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:97537400-97540800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr2:97537800-97544200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:97538000-97541000	Enhancers	Right Ventricle	heart
17	chr2:97538000-97543800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:97538400-97540600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:97538400-97540600	Enhancers	HMEC	breast
20	chr2:97538400-97540800	Enhancers	Left Ventricle	heart
21	chr2:97538400-97541800	Enhancers	Fetal Kidney	kidney
22	chr2:97538400-97542400	Enhancers	Brain Substantia Nigra	brain
23	chr2:97538400-97544400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:97538400-97547400	Enhancers	Spleen	Spleen
25	chr2:97538600-97540600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:97538600-97540600	Enhancers	Pancreas	Pancrea
27	chr2:97538600-97540800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:97538600-97541000	Enhancers	Adipose Nuclei	Adipose
29	chr2:97538600-97541200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:97538600-97541200	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr2:97538600-97541200	Enhancers	Esophagus	oesophagus
32	chr2:97538600-97541800	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr2:97538600-97542000	Enhancers	Fetal Muscle Leg	muscle
34	chr2:97538600-97542400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr2:97538600-97542600	Enhancers	Fetal Stomach	stomach
36	chr2:97538600-97542800	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr2:97538600-97542800	Enhancers	Brain Hippocampus Middle	brain
38	chr2:97538600-97543000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr2:97538600-97543800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
40	chr2:97538600-97544800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr2:97538600-97545000	Enhancers	HSMMtube	muscle
42	chr2:97538800-97540600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:97538800-97540600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr2:97538800-97541000	Enhancers	Duodenum Mucosa	Duodenum
45	chr2:97538800-97541000	Bivalent Enhancer	Fetal Thymus	thymus
46	chr2:97538800-97542400	Enhancers	Brain Cingulate Gyrus	brain
47	chr2:97539000-97541400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:97539000-97541600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr2:97539000-97541600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr2:97539000-97541600	Weak transcription	NH-A	brain

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