Variant report

Variant	rs175878
Chromosome Location	chr12:120122805-120122806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120118680..120120243-chr12:120122175..120124778,2	MCF-7	breast:
2	chr12:120105122..120114412-chr12:120115205..120125435,13	MCF-7	breast:
3	chr12:120121421..120124457-chr12:120131383..120133507,3	K562	blood:
4	chr12:120122749..120126442-chr12:120127143..120130647,6	K562	blood:

Variant related genes	Relation type
ENSG00000111725	Chromatin interaction
ENSG00000248636	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10774503	0.88[CEU][hapmap]
rs10849688	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	1.00[ASN][1000 genomes]
rs11064873	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978107	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	0.83[CEU][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs202983	0.87[MEX][hapmap]
rs278102	0.87[MEX][hapmap];0.81[TSI][hapmap]
rs278123	0.83[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.83[CEU][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278143	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278145	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278152	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278154	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278155	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490267	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301592	0.88[CEU][hapmap]
rs7304996	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311779	0.88[CEU][hapmap]
rs7312321	0.88[CEU][hapmap]
rs7960723	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	0.83[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979627	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804667	0.83[CEU][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs175878	WSB2	cis	cerebellum	SCAN
rs175878	COQ5	cis	parietal	SCAN
rs175878	PXN	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120108200-120161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:120112600-120130400	Weak transcription	Right Atrium	heart
3	chr12:120116800-120201800	Weak transcription	Fetal Heart	heart
4	chr12:120117000-120123200	Weak transcription	Fetal Brain Male	brain
5	chr12:120117000-120145800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:120118800-120124600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:120119200-120123600	Enhancers	Stomach Mucosa	stomach
8	chr12:120119200-120125800	Enhancers	Fetal Kidney	kidney
9	chr12:120119200-120130200	Weak transcription	Brain Angular Gyrus	brain
10	chr12:120119200-120135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:120119200-120141200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:120119400-120124600	Weak transcription	NHEK	skin
13	chr12:120119400-120124800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:120119400-120125200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:120119600-120123200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr12:120119600-120124200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:120119600-120130200	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:120119600-120147000	Weak transcription	Brain Substantia Nigra	brain
19	chr12:120119800-120123400	Weak transcription	Lung	lung
20	chr12:120119800-120124000	Weak transcription	Fetal Thymus	thymus
21	chr12:120119800-120125400	Weak transcription	Hela-S3	cervix
22	chr12:120119800-120149800	Weak transcription	Placenta	Placenta
23	chr12:120120000-120124200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:120120000-120124200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:120120000-120124400	Weak transcription	Fetal Brain Female	brain
26	chr12:120120000-120124400	Weak transcription	Right Ventricle	heart
27	chr12:120120000-120124800	Weak transcription	HMEC	breast
28	chr12:120120000-120129600	Weak transcription	Brain Hippocampus Middle	brain
29	chr12:120120000-120135000	Weak transcription	Esophagus	oesophagus
30	chr12:120120000-120135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr12:120120200-120123200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:120120200-120123400	Weak transcription	Dnd41	blood
33	chr12:120120200-120124200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr12:120120200-120124200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr12:120120200-120124200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr12:120120200-120124200	Weak transcription	Colonic Mucosa	Colon
37	chr12:120120200-120124200	Weak transcription	Gastric	stomach
38	chr12:120120200-120124200	Weak transcription	Stomach Smooth Muscle	stomach
39	chr12:120120200-120124200	Weak transcription	Spleen	Spleen
40	chr12:120120200-120124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:120120200-120124600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:120120200-120124600	Enhancers	Fetal Intestine Large	intestine
43	chr12:120120200-120148000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:120120400-120123000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:120120400-120123400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:120120400-120123800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:120120400-120124000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr12:120120400-120124000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:120120400-120124000	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr12:120120400-120124200	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links