Variant report

Variant	rs35496411
Chromosome Location	chr12:104683290-104683291
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	BRCA1	chr12:104682117-104683361	Hela-S3	cervix:	n/a	n/a
2	GATA3	chr12:104681970-104683989	A549	lung:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683841-104683851 chr12:104683193-104683210
3	POLR2A	chr12:104679566-104684466	PANC-1	pancreas:	n/a	n/a
4	WRNIP1	chr12:104682017-104683835	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:104680676-104684470	A549	lung:	n/a	n/a
6	POLR2A	chr12:104682049-104683470	K562	blood:	n/a	n/a
7	POLR2A	chr12:104679817-104683502	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr12:104679670-104683975	HUVEC	blood vessel:	n/a	n/a
9	GATA3	chr12:104682287-104683460	SK-N-SH	brain:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683193-104683210
10	POLR2A	chr12:104682066-104683608	MCF10A-Er-Src	breast:	n/a	n/a
11	SP1	chr12:104679158-104684055	A549	lung:	n/a	chr12:104682628-104682639 chr12:104683086-104683100
12	BCL3	chr12:104681838-104683936	A549	lung:	n/a	n/a
13	POLR2A	chr12:104683117-104683466	Hela-S3	cervix:	n/a	n/a
14	ELF1	chr12:104682944-104683455	A549	lung:	n/a	chr12:104683082-104683093
15	POLR2A	chr12:104679672-104683881	HepG2	liver:	n/a	n/a
16	MYC	chr12:104682273-104683291	NB4	blood:	n/a	n/a
17	SIN3AK20	chr12:104681904-104684468	A549	lung:	n/a	n/a
18	TAL1	chr12:104682178-104683408	K562	blood:	n/a	n/a
19	TCF12	chr12:104681919-104683573	A549	lung:	n/a	n/a
20	POLR2A	chr12:104681942-104683905	HCT-116	colon:	n/a	n/a
21	GATA2	chr12:104682236-104683462	HUVEC	blood vessel:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683216-104683229 chr12:104683187-104683201 chr12:104683193-104683210
22	TBL1XR1	chr12:104682030-104683344	K562	blood:	n/a	n/a
23	RFX5	chr12:104682046-104683396	Hela-S3	cervix:	n/a	n/a
24	USF2	chr12:104682090-104683422	Hela-S3	cervix:	n/a	n/a
25	MTA3	chr12:104682048-104683494	GM12878	blood:	n/a	n/a
26	MYC	chr12:104682379-104683357	K562	blood:	n/a	n/a
27	POLR2A	chr12:104679831-104683884	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:104680251-104683962	PANC-1	pancreas:	n/a	n/a
29	GATA2	chr12:104682511-104683435	SH-SY5Y	brain:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683216-104683229 chr12:104683187-104683201 chr12:104683193-104683210
30	TAF1	chr12:104680194-104683939	A549	lung:	n/a	n/a
31	USF1	chr12:104681977-104684015	A549	lung:	n/a	n/a
32	MXI1	chr12:104682031-104683330	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr12:104683234-104683304	GM12878	blood:	n/a	n/a
34	ELF1	chr12:104683070-104683470	K562	blood:	n/a	chr12:104683082-104683093
35	ELF1	chr12:104683033-104683482	GM12878	blood:	n/a	chr12:104683082-104683093
36	SIN3AK20	chr12:104681900-104683966	A549	lung:	n/a	n/a
37	POLR2A	chr12:104680118-104683466	H1-hESC	embryonic stem cell:	n/a	n/a
38	SMC3	chr12:104682377-104683396	Hela-S3	cervix:	n/a	n/a
39	SPI1	chr12:104682411-104683482	HL-60	blood:	n/a	chr12:104683087-104683100 chr12:104683089-104683096 chr12:104683224-104683231
40	TBP	chr12:104682039-104683505	Hela-S3	cervix:	n/a	n/a
41	GATA3	chr12:104682347-104683431	T-47D	breast:	n/a	chr12:104683188-104683204 chr12:104683192-104683201 chr12:104683191-104683199 chr12:104683216-104683229 chr12:104683193-104683210
42	EP300	chr12:104679346-104683911	A549	lung:	n/a	chr12:104679847-104679857
43	REST	chr12:104679408-104684472	A549	lung:	n/a	chr12:104680747-104680760
44	ZBTB33	chr12:104681903-104683526	A549	lung:	n/a	n/a
45	MAX	chr12:104681945-104684039	A549	lung:	n/a	n/a
46	HEY1	chr12:104681982-104683744	K562	blood:	n/a	n/a
47	RCOR1	chr12:104682337-104683326	K562	blood:	n/a	n/a
48	ATF3	chr12:104681900-104684118	A549	lung:	n/a	n/a
49	POLR2A	chr12:104682018-104683434	HepG2	liver:	n/a	n/a
50	ELF1	chr12:104681960-104683895	A549	lung:	n/a	chr12:104683082-104683093

No.	Distal block	Cell Line	Cell type
1	chr12:104682529..104684202-chr12:105629338..105630884,2	MCF-7	breast:
2	chr12:104348328..104351209-chr12:104680724..104683661,2	K562	blood:
3	chr12:104680142..104683904-chr12:104694272..104698636,5	MCF-7	breast:
4	chr12:104608375..104610840-chr12:104681920..104683609,3	MCF-7	breast:
5	chr12:104441752..104444274-chr12:104682358..104684016,2	K562	blood:
6	chr12:104606650..104616346-chr12:104679108..104687347,18	K562	blood:
7	chr12:104606650..104611349-chr12:104679680..104683932,8	K562	blood:
8	chr12:104643850..104647465-chr12:104679926..104684172,5	K562	blood:
9	chr12:104530429..104534144-chr12:104679811..104684673,6	MCF-7	breast:
10	chr12:104611527..104621556-chr12:104677756..104684608,20	MCF-7	breast:
11	chr12:104681662..104683943-chr12:104703194..104704714,2	MCF-7	breast:

Variant related genes	Relation type
TXNRD1	TF binding region
ENSG00000204954	Chromatin interaction
ENSG00000136044	Chromatin interaction
ENSG00000198431	Chromatin interaction
ENSG00000120820	Chromatin interaction
ENSG00000120837	Chromatin interaction
ENSG00000255150	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs34244007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34310509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35090883	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35730157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35928066	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55717848	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56139001	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60783408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60836659	1.00[AFR][1000 genomes]
rs61116902	1.00[AFR][1000 genomes];1.00[AMR][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	nsv899493	chr12:104548613-104703228	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv899494	chr12:104561521-104806232	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046606	chr12:104606617-104763734	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1038609	chr12:104613847-104764981	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv541587	chr12:104613847-104764981	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104680000-104683400	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr12:104680000-104683600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104680000-104683800	Active TSS	Aorta	Aorta
4	chr12:104680400-104683400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:104680400-104683400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:104680400-104683600	Active TSS	Brain Anterior Caudate	brain
7	chr12:104680400-104683600	Active TSS	Brain Cingulate Gyrus	brain
8	chr12:104680400-104683600	Active TSS	Brain Hippocampus Middle	brain
9	chr12:104680400-104683600	Active TSS	Fetal Kidney	kidney
10	chr12:104680400-104683600	Active TSS	Left Ventricle	heart
11	chr12:104680400-104683600	Active TSS	Ovary	ovary
12	chr12:104680400-104683600	Active TSS	Psoas Muscle	Psoas
13	chr12:104680400-104683600	Active TSS	Right Ventricle	heart
14	chr12:104680400-104683800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr12:104680400-104684000	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr12:104680400-104684000	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr12:104680400-104684000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr12:104680400-104684200	Active TSS	Right Atrium	heart
19	chr12:104680600-104683400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr12:104680600-104683400	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr12:104680600-104683400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:104680600-104683400	Active TSS	Pancreas	Pancrea
23	chr12:104680600-104683600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr12:104680600-104683600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:104680600-104683600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:104680600-104683600	Active TSS	Colonic Mucosa	Colon
27	chr12:104680600-104683600	Active TSS	Fetal Stomach	stomach
28	chr12:104680600-104683600	Active TSS	Lung	lung
29	chr12:104680600-104683600	Active TSS	Rectal Smooth Muscle	rectum
30	chr12:104680600-104683600	Active TSS	HSMM	muscle
31	chr12:104680600-104683600	Active TSS	NHDF-Ad	bronchial
32	chr12:104680600-104683800	Active TSS	H9 Cell Line	embryonic stem cell
33	chr12:104680600-104683800	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:104680600-104683800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr12:104680600-104683800	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr12:104680600-104684000	Active TSS	GM12878-XiMat	blood
37	chr12:104680600-104684200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:104680600-104684400	Active TSS	Esophagus	oesophagus
39	chr12:104680600-104684600	Active TSS	Hela-S3	cervix
40	chr12:104680800-104683600	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr12:104681200-104683800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr12:104681200-104683800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:104681200-104684000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr12:104681400-104683600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr12:104681400-104684000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:104681600-104683600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr12:104682000-104683800	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr12:104682000-104687400	Transcr. at gene 5' and 3'	A549	lung
49	chr12:104682200-104683400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr12:104682200-104684000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links