Variant report

Variant	rs10844223
Chromosome Location	chr12:32657276-32657277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10506090	0.82[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10506093	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10771960	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10771961	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10771962	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844222	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10844224	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844226	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844227	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844228	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10844229	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10844230	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10844231	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10844234	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11052046	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11052052	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11052053	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11052055	0.81[MEX][hapmap]
rs11608343	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1500875	0.82[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1500876	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17536908	0.81[MEX][hapmap]
rs2133943	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4520681	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61928965	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7308163	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7962342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964715	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7967306	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7967702	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7974089	0.96[AMR][1000 genomes];0.86[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10844223	FGD4	cis	cerebellum	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
2	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
3	chr12:32649600-32658200	Weak transcription	Primary T cells from cord blood	blood
4	chr12:32650800-32659200	Weak transcription	Aorta	Aorta
5	chr12:32651200-32658000	Weak transcription	Primary B cells from cord blood	blood
6	chr12:32651400-32658000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:32654000-32658600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:32654400-32659400	Enhancers	HMEC	breast
9	chr12:32654800-32658000	Active TSS	Brain Anterior Caudate	brain
10	chr12:32654800-32658000	Active TSS	Brain Germinal Matrix	brain
11	chr12:32654800-32658600	Active TSS	Fetal Muscle Trunk	muscle
12	chr12:32655000-32657400	Active TSS	HSMM	muscle
13	chr12:32655000-32658800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:32655000-32658800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:32655200-32661600	Weak transcription	Spleen	Spleen
16	chr12:32655200-32686000	Weak transcription	Lung	lung
17	chr12:32655400-32661000	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:32655800-32659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:32656000-32658000	Weak transcription	Small Intestine	intestine
20	chr12:32656000-32658600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:32656000-32659200	Enhancers	Adipose Nuclei	Adipose
22	chr12:32656000-32661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:32656000-32666000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
25	chr12:32656200-32657400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:32656200-32658200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr12:32656200-32658200	Weak transcription	Fetal Kidney	kidney
28	chr12:32656200-32659800	Enhancers	H1 Cell Line	embryonic stem cell
29	chr12:32656200-32662600	Weak transcription	HepG2	liver
30	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:32656400-32657400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:32656400-32657400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:32656400-32657400	Enhancers	HUVEC	blood vessel
34	chr12:32656400-32657800	Weak transcription	NHDF-Ad	bronchial
35	chr12:32656400-32658000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr12:32656400-32659400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr12:32656400-32659400	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr12:32656400-32659800	Enhancers	Fetal Lung	lung
39	chr12:32656400-32660000	Enhancers	Fetal Intestine Small	intestine
40	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr12:32656600-32657400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:32656600-32657400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr12:32656600-32657600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr12:32656600-32658400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:32656800-32657600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr12:32656800-32657800	Enhancers	Muscle Satellite Cultured Cells	--
47	chr12:32656800-32658200	Flanking Active TSS	HSMMtube	muscle
48	chr12:32656800-32659000	Enhancers	Stomach Mucosa	stomach
49	chr12:32656800-32659800	Enhancers	Fetal Intestine Large	intestine
50	chr12:32657000-32657400	Flanking Active TSS	Liver	Liver

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