Variant report

Variant	rs10844000
Chromosome Location	chr12:31864244-31864245
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31860661..31864274-chr12:31866939..31870536,4	K562	blood:
2	chr12:31863317..31864932-chr12:31883835..31885754,2	K562	blood:

Variant related genes	Relation type
ENSG00000151743	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10844047	1.00[YRI][hapmap]
rs11051525	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11051541	0.95[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11051545	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes]
rs11051559	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs12367895	0.85[AMR][1000 genomes]
rs12813042	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12813399	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12813695	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[YRI][hapmap]
rs35517071	0.84[AMR][1000 genomes]
rs3850979	0.84[ASW][hapmap]
rs7297921	0.83[AMR][1000 genomes]
rs7300260	1.00[ASW][hapmap];0.95[CEU][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7302229	0.81[AMR][1000 genomes]
rs7960893	0.84[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7969019	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[YRI][hapmap]
rs7978407	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv898967	chr12:31858031-31899475	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10844000	AMN1	cis	cerebellum	SCAN
rs10844000	C12orf72	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31822600-31874200	Weak transcription	Right Ventricle	heart
2	chr12:31827000-31871800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:31837200-31865000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:31838600-31881000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr12:31839800-31871800	Weak transcription	Gastric	stomach
6	chr12:31841600-31870000	Weak transcription	Pancreas	Pancrea
7	chr12:31844600-31871800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:31846400-31871800	Weak transcription	Lung	lung
9	chr12:31849000-31880000	Weak transcription	Psoas Muscle	Psoas
10	chr12:31850800-31867600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:31851000-31880800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:31852800-31871000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:31852800-31879600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:31853000-31867200	Weak transcription	Brain Anterior Caudate	brain
15	chr12:31854600-31867400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr12:31854800-31867600	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:31855000-31867600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:31855400-31867600	Weak transcription	Stomach Mucosa	stomach
19	chr12:31858000-31867600	Weak transcription	A549	lung
20	chr12:31858000-31867800	Weak transcription	HUVEC	blood vessel
21	chr12:31859000-31871800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr12:31859800-31864400	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:31860400-31872400	Weak transcription	Fetal Kidney	kidney
24	chr12:31860600-31874000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:31860800-31871800	Weak transcription	Ovary	ovary
26	chr12:31860800-31881000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:31861000-31871800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr12:31862200-31880600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:31862400-31871800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:31862600-31864400	Weak transcription	Brain Germinal Matrix	brain
31	chr12:31862600-31867400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:31862600-31867800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:31862600-31868000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr12:31862600-31868200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr12:31862600-31868400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:31862600-31871200	Weak transcription	Fetal Lung	lung
37	chr12:31862600-31871800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:31862800-31865000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:31862800-31865600	Weak transcription	Fetal Intestine Small	intestine
40	chr12:31862800-31865800	Weak transcription	Fetal Thymus	thymus
41	chr12:31862800-31867200	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr12:31862800-31867600	Weak transcription	Primary T cells from cord blood	blood
43	chr12:31862800-31867600	Weak transcription	Thymus	Thymus
44	chr12:31862800-31871800	Weak transcription	Aorta	Aorta
45	chr12:31862800-31874200	Weak transcription	Left Ventricle	heart
46	chr12:31863800-31867400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:31863800-31868000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr12:31864000-31867400	Weak transcription	Primary B cells from cord blood	blood
49	chr12:31864000-31871800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:31864200-31867400	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links