Variant report

Variant	rs775249
Chromosome Location	chr12:57977003-57977004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:57976238..57978817-chr12:58135454..58137722,2	MCF-7	breast:
2	chr12:57976847..57977730-chr12:58004752..58005632,2	MCF-7	breast:
3	chr12:57976840..57977702-chr12:58176102..58176863,2	K562	blood:
4	chr12:57975970..57978531-chr12:58137833..58141150,3	MCF-7	breast:
5	chr12:57976849..57977696-chr12:58026398..58026930,2	MCF-7	breast:
6	chr12:57976787..57977771-chr12:58135919..58136902,3	MCF-7	breast:
7	chr12:57976772..57979526-chr12:58013170..58016217,4	MCF-7	breast:
8	chr12:57976905..57977643-chr12:58129262..58129943,2	MCF-7	breast:
9	chr12:57975136..57977432-chr12:58144177..58146349,2	K562	blood:
10	chr12:57976942..57977694-chr12:58014849..58016025,6	MCF-7	breast:
11	chr12:57970575..57973134-chr12:57976795..57978927,2	K562	blood:
12	chr12:57976014..57978875-chr12:57984768..57986490,2	K562	blood:
13	chr12:57976712..57977327-chr12:58017523..58018221,2	MCF-7	breast:
14	chr12:57976485..57979398-chr12:58012165..58015688,3	MCF-7	breast:
15	chr12:57976679..57977833-chr12:58015073..58017142,20	MCF-7	breast:
16	chr12:57908786..57911403-chr12:57975787..57979264,3	K562	blood:
17	chr12:57976768..57977773-chr12:58026595..58027466,5	K562	blood:
18	chr12:57976760..57978150-chr12:58015081..58016157,16	K562	blood:
19	chr12:57976724..57977517-chr12:58016494..58017081,2	MCF-7	breast:
20	chr12:57976837..57977750-chr12:58129328..58130470,7	MCF-7	breast:
21	chr12:57976987..57977741-chr12:58026501..58027421,5	MCF-7	breast:
22	chr12:57976568..57977825-chr12:58129195..58130317,11	K562	blood:

No data

Variant related genes	Relation type
ENSG00000166908	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135439	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000135446	Chromatin interaction
ENSG00000135454	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000135502	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11172256	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs775246	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775248	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs775250	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8873	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
3	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
6	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
7	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
8	nsv541504	chr12:57958701-58062311	Bivalent Enhancer Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv725	chr12:57966549-57993808	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	n/a

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs775249	ARHGAP9	cis	lymphoblastoid	seeQTL
rs775249	ARHGEF25	cis	parietal	SCAN
rs775249	PPP1R1A	cis	parietal	SCAN
rs775249	ARHGAP9	cis	cerebellum	SCAN
rs775249	ARHGEF25	cis	cerebellum	SCAN
rs775249	KRT7	cis	cerebellum	SCAN
rs775249	AMHR2	cis	cerebellum	SCAN
rs775249	MARCH9	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57956600-57980600	Strong transcription	Brain Germinal Matrix	brain
2	chr12:57957000-57980800	Strong transcription	Fetal Brain Female	brain
3	chr12:57957200-57979200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:57961000-57982000	Weak transcription	Right Atrium	heart
5	chr12:57962200-57978200	Weak transcription	Spleen	Spleen
6	chr12:57964400-57984400	Weak transcription	Pancreas	Pancrea
7	chr12:57966400-57984000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:57966600-57984000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:57966600-57984600	Weak transcription	Gastric	stomach
10	chr12:57966800-57984400	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr12:57967200-57982000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:57968800-57977200	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr12:57969000-57978600	Strong transcription	K562	blood
14	chr12:57970600-57984200	Weak transcription	Fetal Brain Male	brain
15	chr12:57971600-57978200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr12:57972200-57984200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:57972200-57984400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr12:57972600-57980800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr12:57975600-57984200	Weak transcription	Brain Substantia Nigra	brain
20	chr12:57975800-57977400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr12:57975800-57977400	Weak transcription	Brain Hippocampus Middle	brain
22	chr12:57975800-57978200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:57975800-57979800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:57975800-57984200	Weak transcription	Brain Angular Gyrus	brain
25	chr12:57975800-57984400	Weak transcription	Aorta	Aorta
26	chr12:57976000-57978200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr12:57976000-57980000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:57976000-57980200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr12:57976200-57984200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr12:57976400-57984400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:57976600-57984200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:57976800-57977200	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr12:57976800-57977200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
34	chr12:57976800-57977400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
35	chr12:57976800-57977600	Enhancers	Dnd41	blood
36	chr12:57976800-57977800	Genic enhancers	HepG2	liver
37	chr12:57976800-57978400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:57976800-57984200	Weak transcription	Brain Anterior Caudate	brain
39	chr12:57977000-57977200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
40	chr12:57977000-57977200	Enhancers	Liver	Liver
41	chr12:57977000-57977400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
42	chr12:57977000-57977400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:57977000-57977600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr12:57977000-57977600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
45	chr12:57977000-57977600	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr12:57977000-57977600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr12:57977000-57977800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:57977000-57978200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:57977000-57981600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:57977000-57981600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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