Variant report

Variant	rs7575177
Chromosome Location	chr2:153373895-153373896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11678890	0.94[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17327752	0.87[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17399648	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35552611	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4664114	0.81[MEX][hapmap]
rs4664591	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706231	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749146	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6760321	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9753431	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv834419	chr2:153179420-153381476	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	esv3693436	chr2:153219836-153479857	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1013777	chr2:153273637-153538546	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv834420	chr2:153339646-153535460	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7575177	CACNB4	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153357400-153375200	Weak transcription	Right Atrium	heart
2	chr2:153361000-153398600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:153362400-153379400	Weak transcription	Fetal Brain Male	brain
4	chr2:153365000-153377600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:153365400-153377200	Weak transcription	Small Intestine	intestine
6	chr2:153365600-153375200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:153365600-153386000	Weak transcription	Fetal Stomach	stomach
8	chr2:153368400-153374600	Enhancers	Brain Substantia Nigra	brain
9	chr2:153368600-153375200	Enhancers	Brain Cingulate Gyrus	brain
10	chr2:153370400-153375200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:153370400-153375400	Weak transcription	NH-A	brain
12	chr2:153370600-153374400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:153370600-153374400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr2:153370600-153375000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:153370600-153375200	Weak transcription	Aorta	Aorta
16	chr2:153370600-153375200	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:153370600-153375600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:153370800-153374200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:153370800-153375200	Enhancers	Brain Hippocampus Middle	brain
20	chr2:153370800-153375800	Weak transcription	Osteobl	bone
21	chr2:153371000-153374200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr2:153371000-153374400	Weak transcription	HMEC	breast
23	chr2:153371000-153374600	Weak transcription	A549	lung
24	chr2:153371000-153375200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:153371000-153375800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:153371000-153379200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:153371600-153375200	Weak transcription	Psoas Muscle	Psoas
28	chr2:153372200-153374200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:153372200-153375200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:153372400-153374400	Weak transcription	Brain Anterior Caudate	brain
31	chr2:153373000-153380200	Weak transcription	Brain Germinal Matrix	brain
32	chr2:153373800-153375400	Enhancers	HepG2	liver
33	chr2:153373800-153375600	Enhancers	Ovary	ovary
34	chr2:153373800-153375800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr2:153373800-153376200	Enhancers	NHEK	skin
36	chr2:153373800-153376400	Enhancers	Brain Angular Gyrus	brain
37	chr2:153373800-153377600	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links