Variant report

Variant	rs1875311
Chromosome Location	chr12:32651839-32651840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10506092	1.00[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052034	0.85[JPT][hapmap]
rs12830147	0.98[ASN][1000 genomes]
rs16919947	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16919964	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16919969	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16920000	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2047642	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34174269	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34792203	0.98[ASN][1000 genomes]
rs35563266	0.81[ASN][1000 genomes]
rs35590458	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35885876	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56838031	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60069665	0.98[ASN][1000 genomes]
rs67649350	0.83[ASN][1000 genomes]
rs7297744	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305247	0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs7311935	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315682	0.87[CHD][hapmap]
rs7966521	0.81[ASW][hapmap];0.87[CHD][hapmap]
rs7967302	0.90[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1875311	FGD4	cis	cerebellum	SCAN
rs1875311	ERGIC2	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
2	chr12:32621800-32654000	Weak transcription	Lung	lung
3	chr12:32625000-32655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:32625200-32655200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:32634000-32655000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:32639000-32655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:32639400-32653800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:32639400-32653800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:32639400-32653800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:32641200-32653800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr12:32644000-32653800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr12:32644800-32654400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:32646000-32653800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:32646200-32654200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr12:32646600-32652600	Weak transcription	Left Ventricle	heart
16	chr12:32646600-32653800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:32646600-32653800	Weak transcription	Gastric	stomach
18	chr12:32646600-32654000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:32647200-32653000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:32647800-32653800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:32647800-32654000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:32648000-32652000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:32648000-32652000	Weak transcription	HUVEC	blood vessel
24	chr12:32648000-32653800	Weak transcription	Spleen	Spleen
25	chr12:32648000-32654200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:32648200-32653600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:32648200-32653800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:32648200-32653800	Weak transcription	Adipose Nuclei	Adipose
29	chr12:32648200-32654400	Weak transcription	HMEC	breast
30	chr12:32648200-32655600	Weak transcription	NHEK	skin
31	chr12:32648200-32657200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:32648800-32653800	Weak transcription	Right Atrium	heart
33	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
34	chr12:32649200-32653800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:32649600-32658200	Weak transcription	Primary T cells from cord blood	blood
36	chr12:32649800-32652400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:32650000-32652600	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:32650400-32652800	Enhancers	Stomach Mucosa	stomach
39	chr12:32650600-32652800	Enhancers	Psoas Muscle	Psoas
40	chr12:32650600-32656200	Enhancers	Fetal Heart	heart
41	chr12:32650800-32653800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:32650800-32659200	Weak transcription	Aorta	Aorta
43	chr12:32651000-32652200	Enhancers	Pancreas	Pancrea
44	chr12:32651000-32653800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr12:32651000-32654000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:32651000-32654600	Weak transcription	Brain Angular Gyrus	brain
47	chr12:32651000-32654800	Enhancers	Fetal Intestine Small	intestine
48	chr12:32651200-32653800	Weak transcription	Brain Substantia Nigra	brain
49	chr12:32651200-32653800	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:32651200-32653800	Weak transcription	Ovary	ovary

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