Variant report

Variant	rs10844457
Chromosome Location	chr12:9842008-9842009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9798180..9800889-chr12:9840651..9843314,2	K562	blood:
2	chr12:9787751..9790027-chr12:9840631..9842655,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256442	Chromatin interaction
ENSG00000256594	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1008611	0.84[ASN][1000 genomes]
rs10743821	0.84[ASN][1000 genomes]
rs10743822	0.84[ASN][1000 genomes]
rs10844418	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10844424	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844429	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844449	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844476	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052303	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052304	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11052305	0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052311	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052327	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052342	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052366	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052367	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052369	0.80[AFR][1000 genomes]
rs11052430	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052431	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052434	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052718	0.84[ASN][1000 genomes]
rs11052785	0.84[ASN][1000 genomes]
rs11519377	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11524523	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12301473	0.80[AFR][1000 genomes]
rs12309762	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12312233	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs12320830	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12578698	0.84[ASN][1000 genomes]
rs12578928	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12582616	0.84[ASN][1000 genomes]
rs12810851	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815393	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12817365	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12825507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828602	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12828773	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12831453	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990533	0.84[ASN][1000 genomes]
rs2114872	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2114873	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192433	0.84[ASN][1000 genomes]
rs2192434	0.84[ASN][1000 genomes]
rs2192435	0.84[ASN][1000 genomes]
rs2192439	0.89[ASN][1000 genomes]
rs2401396	0.84[ASN][1000 genomes]
rs34201389	0.84[ASN][1000 genomes]
rs35237063	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763264	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4763835	0.84[ASN][1000 genomes]
rs61913428	0.84[ASN][1000 genomes]
rs6488109	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6488122	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310897	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7954062	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7969074	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7972035	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7979758	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630264	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630265	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668568	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs982511	0.84[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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10844457	LOC374443	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
4	chr12:9826400-9849000	Weak transcription	Psoas Muscle	Psoas
5	chr12:9826600-9847200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:9826600-9852400	Weak transcription	Colon Smooth Muscle	Colon
7	chr12:9826800-9844600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:9826800-9848400	Weak transcription	Colonic Mucosa	Colon
9	chr12:9826800-9849400	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr12:9826800-9849800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:9826800-9854400	Weak transcription	Esophagus	oesophagus
12	chr12:9827000-9853200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:9827200-9847000	Weak transcription	NH-A	brain
14	chr12:9827200-9847400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:9827200-9847600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:9827200-9851000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:9827200-9851600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:9827200-9852400	Weak transcription	Osteobl	bone
19	chr12:9827400-9849000	Weak transcription	A549	lung
20	chr12:9832800-9846000	Weak transcription	Gastric	stomach
21	chr12:9833000-9849000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:9833200-9847200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:9835400-9849200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr12:9835800-9847000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:9836000-9843000	Weak transcription	Liver	Liver
26	chr12:9837000-9847400	Weak transcription	Fetal Brain Female	brain
27	chr12:9837600-9842400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:9837800-9846800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr12:9837800-9849400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr12:9838200-9849800	Strong transcription	Fetal Thymus	thymus
31	chr12:9838400-9844800	Weak transcription	Left Ventricle	heart
32	chr12:9838400-9849600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr12:9838600-9843000	ZNF genes & repeats	GM12878-XiMat	blood
34	chr12:9838800-9842800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:9838800-9846200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:9838800-9849200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:9838800-9854400	Weak transcription	Spleen	Spleen
38	chr12:9839000-9854400	Weak transcription	Lung	lung
39	chr12:9839400-9842200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:9839400-9848800	Weak transcription	Brain Substantia Nigra	brain
41	chr12:9839400-9854600	Weak transcription	Small Intestine	intestine
42	chr12:9839600-9846200	Weak transcription	HepG2	liver
43	chr12:9839800-9844400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:9840000-9842400	Strong transcription	Fetal Intestine Large	intestine
45	chr12:9840000-9849000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:9840200-9842200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:9840200-9842200	Weak transcription	NHDF-Ad	bronchial
48	chr12:9840200-9842800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:9840200-9848200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr12:9840400-9842600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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