Variant report

Variant	rs12548040
Chromosome Location	chr8:121729069-121729070
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	chr8:121721252..121724174-chr8:121726884..121729433,3	MCF-7	breast:
2	chr8:68133026..68135456-chr8:121726953..121729771,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11985259	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs11995748	1.00[CEU][hapmap]
rs11997006	0.81[CHB][hapmap]
rs12541284	0.80[ASN][1000 genomes]
rs12542152	0.82[ASN][1000 genomes]
rs12542405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543043	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12543097	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546661	0.80[ASN][1000 genomes]
rs12547255	0.80[ASN][1000 genomes]
rs12547287	0.80[ASN][1000 genomes]
rs4242320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4242322	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4242323	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4304359	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4609235	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4870750	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4871101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4871103	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4871105	0.80[ASN][1000 genomes]
rs4871106	0.80[ASN][1000 genomes]
rs4871107	0.80[ASN][1000 genomes]
rs4871109	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4871119	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4871122	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4871124	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs4871125	0.87[GIH][hapmap];0.81[MEX][hapmap]
rs55723447	0.80[ASN][1000 genomes]
rs57196351	0.80[ASN][1000 genomes]
rs57785870	0.80[ASN][1000 genomes]
rs58528057	0.80[ASN][1000 genomes]
rs59495531	0.80[ASN][1000 genomes]
rs59586775	0.80[ASN][1000 genomes]
rs61063678	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73321282	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73321301	0.80[ASN][1000 genomes]
rs73321302	0.80[ASN][1000 genomes]
rs73323116	0.80[ASN][1000 genomes]
rs73710013	0.80[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	nsv1016172	chr8:121679590-121929916	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv891422	chr8:121680857-121819478	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12548040	DSCC1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:121714800-121729400	Weak transcription	Right Atrium	heart
2	chr8:121719400-121736600	Weak transcription	HSMM	muscle
3	chr8:121719600-121736400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr8:121719600-121739000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr8:121719800-121729400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr8:121720000-121729400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr8:121722800-121737000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr8:121723000-121729600	Weak transcription	Left Ventricle	heart
9	chr8:121723000-121730800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr8:121723000-121731400	Weak transcription	Fetal Thymus	thymus
11	chr8:121723000-121734200	Weak transcription	Aorta	Aorta
12	chr8:121723400-121737000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr8:121723800-121729400	Weak transcription	Lung	lung
14	chr8:121723800-121730200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr8:121725400-121730600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr8:121725400-121736800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr8:121726000-121729400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr8:121726200-121729400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr8:121726200-121729400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr8:121726400-121729800	Strong transcription	HepG2	liver
21	chr8:121726400-121731800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr8:121726600-121731800	Weak transcription	Primary B cells from cord blood	blood
23	chr8:121727000-121729400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr8:121727000-121730400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr8:121727200-121729400	Weak transcription	HSMMtube	muscle
26	chr8:121727400-121729200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:121727400-121729800	Weak transcription	Fetal Lung	lung
28	chr8:121727400-121730800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr8:121727600-121729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr8:121727600-121730200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr8:121727600-121730600	Weak transcription	Liver	Liver
32	chr8:121727600-121730800	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr8:121727800-121729400	Weak transcription	Adipose Nuclei	Adipose
34	chr8:121727800-121729400	Weak transcription	Brain Anterior Caudate	brain
35	chr8:121727800-121729400	Weak transcription	NHLF	lung
36	chr8:121727800-121729800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr8:121727800-121731000	Enhancers	Fetal Muscle Leg	muscle
38	chr8:121728000-121730600	Enhancers	Ovary	ovary
39	chr8:121728200-121729400	Weak transcription	Spleen	Spleen
40	chr8:121728200-121730600	Enhancers	Psoas Muscle	Psoas
41	chr8:121728200-121736000	Weak transcription	Primary T cells from cord blood	blood
42	chr8:121728400-121730000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr8:121728400-121730000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr8:121728400-121730800	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr8:121729000-121729400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr8:121729000-121729800	Weak transcription	Colon Smooth Muscle	Colon
47	chr8:121729000-121739200	Weak transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links