Variant report

Variant	rs9863
Chromosome Location	chr12:124421453-124421454
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:124419696..124421587-chr12:124455495..124458360,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119242	Chromatin interaction
ENSG00000178882	Chromatin interaction
ENSG00000270095	Chromatin interaction
ENSG00000179195	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10846577	0.92[CHB][hapmap]
rs10846578	1.00[CHB][hapmap]
rs10846579	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10846580	0.81[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057393	0.83[ASN][1000 genomes]
rs11057394	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057396	0.80[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.83[MEX][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11057397	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11057399	0.85[EUR][1000 genomes]
rs11057400	0.93[EUR][1000 genomes]
rs11057401	0.88[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs11057407	0.92[EUR][1000 genomes]
rs11057408	0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs11057409	0.81[CEU][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs11057412	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs11057413	0.84[EUR][1000 genomes]
rs11831913	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs11833002	0.86[EUR][1000 genomes]
rs11835839	0.86[EUR][1000 genomes]
rs11837287	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1187415	0.81[CEU][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs12296259	0.86[EUR][1000 genomes]
rs12298484	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12301673	0.85[EUR][1000 genomes]
rs12303671	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs12303933	0.83[EUR][1000 genomes]
rs12310367	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12311114	0.88[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs12311848	0.83[EUR][1000 genomes]
rs12316080	0.84[EUR][1000 genomes]
rs12317176	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12809125	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12809473	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs12823740	0.81[CEU][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap]
rs12824567	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs12827409	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12829951	0.85[EUR][1000 genomes]
rs12833624	0.84[EUR][1000 genomes]
rs1882491	0.91[EUR][1000 genomes]
rs2130382	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2178663	0.88[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs3186071	0.93[EUR][1000 genomes]
rs34114498	0.84[EUR][1000 genomes]
rs34180676	0.91[EUR][1000 genomes]
rs34854841	0.93[EUR][1000 genomes]
rs34878139	0.86[EUR][1000 genomes]
rs35099862	0.84[EUR][1000 genomes]
rs35825716	0.93[EUR][1000 genomes]
rs3789967	0.85[EUR][1000 genomes]
rs3802999	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4405410	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs4575361	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4765127	0.81[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs4765148	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs4765219	0.81[CEU][hapmap];0.86[GIH][hapmap];0.85[EUR][1000 genomes]
rs4765305	0.86[EUR][1000 genomes]
rs4765335	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4765528	0.88[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4765541	0.85[EUR][1000 genomes]
rs4765562	0.85[EUR][1000 genomes]
rs4930721	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4930722	0.93[EUR][1000 genomes]
rs4930723	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs4930724	0.82[ASW][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4930725	0.85[EUR][1000 genomes]
rs4930726	0.81[CEU][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56041971	0.83[EUR][1000 genomes]
rs6488912	0.86[EUR][1000 genomes]
rs6488913	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs6488914	0.88[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs7131882	0.85[EUR][1000 genomes]
rs7132655	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs7133378	1.00[CHB][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs7134121	0.84[EUR][1000 genomes]
rs7135314	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs71458830	0.83[EUR][1000 genomes]
rs7301953	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305864	0.90[GIH][hapmap];0.85[EUR][1000 genomes]
rs7307053	0.88[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs7307277	0.81[CEU][hapmap];0.86[GIH][hapmap];0.84[EUR][1000 genomes]
rs7311233	0.88[CEU][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs7311969	0.81[CEU][hapmap];0.82[GIH][hapmap];0.85[EUR][1000 genomes]
rs7312404	0.81[CEU][hapmap];0.90[GIH][hapmap];0.85[EUR][1000 genomes]
rs7955815	0.93[EUR][1000 genomes]
rs7958691	0.85[EUR][1000 genomes]
rs7961449	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs7966192	0.86[EUR][1000 genomes]
rs7973683	0.81[CEU][hapmap];0.86[GIH][hapmap];0.85[EUR][1000 genomes]
rs7975482	0.81[CEU][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs7978610	0.81[CEU][hapmap];0.85[GIH][hapmap];0.83[EUR][1000 genomes]
rs952632	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs9971695	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9863	CCDC92	cis	cerebellum	SCAN
rs9863	ARL6IP4	cis	cerebellum	SCAN
rs9863	COQ5	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124407400-124422000	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:124408800-124428000	Weak transcription	Right Atrium	heart
3	chr12:124409600-124426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:124415000-124423000	Weak transcription	HSMM	muscle
5	chr12:124417200-124421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr12:124417200-124424400	Weak transcription	Colonic Mucosa	Colon
7	chr12:124417400-124421800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:124417400-124421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr12:124417400-124421800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:124417400-124421800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:124417400-124421800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr12:124417400-124422000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:124417600-124443600	Weak transcription	Fetal Kidney	kidney
14	chr12:124417800-124422000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr12:124417800-124427400	Weak transcription	Fetal Brain Male	brain
16	chr12:124417800-124428400	Strong transcription	Brain Germinal Matrix	brain
17	chr12:124418000-124428400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:124418000-124431000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:124418200-124422000	Weak transcription	Dnd41	blood
20	chr12:124418200-124426200	Strong transcription	Fetal Intestine Small	intestine
21	chr12:124418200-124427800	Strong transcription	Fetal Brain Female	brain
22	chr12:124418200-124430800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr12:124418200-124431400	Strong transcription	Fetal Stomach	stomach
24	chr12:124418400-124422200	Strong transcription	Brain Cingulate Gyrus	brain
25	chr12:124418600-124422400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:124418600-124430800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:124418800-124422000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr12:124418800-124422200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:124418800-124422800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr12:124419000-124421800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr12:124419000-124422000	Strong transcription	Placenta	Placenta
32	chr12:124419000-124422400	Strong transcription	Aorta	Aorta
33	chr12:124419000-124428400	Strong transcription	Fetal Muscle Leg	muscle
34	chr12:124419200-124421800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:124419200-124422000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr12:124419200-124422200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr12:124419200-124422400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:124419200-124422400	Strong transcription	Adipose Nuclei	Adipose
39	chr12:124419200-124422600	Strong transcription	Brain Substantia Nigra	brain
40	chr12:124419200-124422800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr12:124419200-124423000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:124419200-124426200	Weak transcription	Fetal Heart	heart
43	chr12:124419400-124421600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:124419400-124422000	Strong transcription	Brain Anterior Caudate	brain
45	chr12:124419400-124422000	Strong transcription	Spleen	Spleen
46	chr12:124419400-124426400	Weak transcription	A549	lung
47	chr12:124419600-124421600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:124419600-124422000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:124419600-124422200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:124419800-124422200	Strong transcription	Osteobl	bone

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