Variant report

Variant	rs2335232
Chromosome Location	chr12:49670029-49670030
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:49664684-49670620	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:49669475-49670041	ECC-1	luminal epithelium:	n/a	n/a
3	FOS	chr12:49669812-49670110	MCF10A-Er-Src	breast:	n/a	n/a
4	NR2F2	chr12:49669984-49671293	MCF-7	breast:	n/a	n/a
5	POLR2A	chr12:49664707-49670365	U87	brain:	n/a	n/a
6	FOS	chr12:49669851-49670033	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:49666509-49670373	U87	brain:	n/a	n/a
8	FOS	chr12:49669872-49670071	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:49658323-49670206	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr12:49666501-49670365	U87	brain:	n/a	n/a
11	POLR2A	chr12:49669540-49670104	MCF-7	breast:	n/a	n/a
12	GATA3	chr12:49670029-49670586	MCF-7	breast:	n/a	n/a
13	BCL3	chr12:49669253-49670159	A549	lung:	n/a	chr12:49669654-49669667
14	POLR2A	chr12:49664636-49670373	U87	brain:	n/a	n/a
15	FOS	chr12:49669814-49670049	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr12:49666482-49670130	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49667022..49671096-chr12:49685141..49687523,3	K562	blood:
2	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
3	chr12:49668999..49670991-chr12:49736933..49738497,2	K562	blood:
4	chr12:49666275..49670972-chr12:49688443..49691988,7	K562	blood:
5	chr12:49669514..49671024-chr12:49690193..49692290,2	MCF-7	breast:
6	chr12:49668673..49670356-chr12:49689589..49691527,2	K562	blood:
7	chr12:49668500..49671128-chr12:49928861..49931681,2	MCF-7	breast:
8	chr12:49523127..49526155-chr12:49667398..49671055,3	K562	blood:
9	chr12:49667913..49670211-chr12:49679594..49681611,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258232	TF binding region
ENSG00000258017	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000135406	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10875941	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875942	0.94[ASW][hapmap];0.95[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.98[LWK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11168936	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2335451	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap]
rs3847766	0.91[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs3858586	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3858587	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7307435	0.95[CEU][hapmap];0.80[YRI][hapmap]
rs7974831	0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2335232	PRPH	cis	cerebellum	SCAN
rs2335232	ATF1	cis	cerebellum	SCAN
rs2335232	MCRS1	cis	cerebellum	SCAN
rs2335232	WNT10B	cis	parietal	SCAN
rs2335232	LARP4	cis	parietal	SCAN
rs2335232	POU6F1	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49659200-49673600	Weak transcription	Fetal Brain Male	brain
2	chr12:49659600-49673600	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:49661600-49670600	Weak transcription	Psoas Muscle	Psoas
4	chr12:49662800-49673400	Weak transcription	Brain Anterior Caudate	brain
5	chr12:49662800-49673400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:49662800-49673400	Weak transcription	Brain Substantia Nigra	brain
7	chr12:49665200-49673200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:49665400-49673800	Weak transcription	Fetal Kidney	kidney
9	chr12:49665600-49673400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr12:49665600-49673400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:49666000-49670800	Weak transcription	Small Intestine	intestine
12	chr12:49666000-49673400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:49666800-49671200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:49667200-49670400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:49667200-49673200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:49667400-49670600	Weak transcription	Hela-S3	cervix
17	chr12:49667400-49671000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr12:49667400-49671200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr12:49667400-49673400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:49667400-49673400	Weak transcription	Pancreas	Pancrea
21	chr12:49667600-49670800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:49667600-49673400	Weak transcription	Left Ventricle	heart
23	chr12:49667600-49673600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:49667800-49670200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:49667800-49670600	Weak transcription	Liver	Liver
26	chr12:49667800-49670800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:49667800-49670800	Weak transcription	Dnd41	blood
28	chr12:49667800-49671200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:49667800-49671200	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:49667800-49671200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr12:49667800-49671200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:49667800-49671400	Weak transcription	K562	blood
33	chr12:49667800-49673200	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:49667800-49673200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:49667800-49673200	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr12:49667800-49673400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:49667800-49673400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:49667800-49673400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:49667800-49673400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr12:49667800-49673400	Weak transcription	Esophagus	oesophagus
41	chr12:49667800-49673400	Weak transcription	Fetal Intestine Large	intestine
42	chr12:49668000-49670200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:49668000-49670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr12:49668000-49670400	Weak transcription	Fetal Thymus	thymus
45	chr12:49668000-49670400	Weak transcription	NHDF-Ad	bronchial
46	chr12:49668000-49670400	Weak transcription	Osteobl	bone
47	chr12:49668000-49671000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:49668000-49671000	Weak transcription	HUVEC	blood vessel
49	chr12:49668000-49671400	Weak transcription	Placenta	Placenta
50	chr12:49668000-49673400	Weak transcription	H1 Cell Line	embryonic stem cell

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