Variant report

Variant	rs844046
Chromosome Location	chr12:42478413-42478414
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	chr12:42477798..42480028-chr12:42482266..42483853,2	K562	blood:
2	chr12:42477955..42479692-chr12:42628844..42631560,2	K562	blood:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	GXYLT1	hsa-miR-124-3p	chr12:42478397-42478414

Variant related genes	Relation type
ENSG00000015153	Chromatin interaction
GXYLT1	miRNA target site

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1024700	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1069644	0.93[JPT][hapmap]
rs10880275	0.93[JPT][hapmap]
rs10880279	0.93[JPT][hapmap]
rs1226303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1233992	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1233994	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1233996	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1238290	0.93[JPT][hapmap]
rs12826710	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1463613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1628871	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1683198	0.82[AMR][1000 genomes]
rs1688855	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1688874	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1688879	0.81[AMR][1000 genomes]
rs1732350	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1732351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1732352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1882139	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1994284	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3852592	0.81[AMR][1000 genomes]
rs6582378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6582392	0.93[JPT][hapmap]
rs712106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs712119	0.93[JPT][hapmap]
rs712120	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs712122	0.93[JPT][hapmap]
rs712123	0.93[JPT][hapmap]
rs712125	0.93[JPT][hapmap]
rs712129	0.93[JPT][hapmap]
rs7136038	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7303028	1.00[CEU][hapmap]
rs7305763	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7956016	0.93[JPT][hapmap]
rs7960176	0.93[JPT][hapmap]
rs7970115	0.87[JPT][hapmap]
rs824697	0.81[AMR][1000 genomes]
rs824699	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs824716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs824717	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs824718	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs824722	0.82[AMR][1000 genomes]
rs824724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs824726	0.81[AMR][1000 genomes]
rs824734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs824738	0.95[CEU][hapmap];0.93[JPT][hapmap]
rs824741	0.93[JPT][hapmap]
rs865420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs917666	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1047830	chr12:42466192-42497603	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3449729	chr12:42477382-42478413	Weak transcription Enhancers Strong transcription Active TSS	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
4	esv3410033	chr12:42478138-42478733	Weak transcription Strong transcription Enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42464600-42484000	Weak transcription	HSMM	muscle
2	chr12:42468400-42490200	Weak transcription	Spleen	Spleen
3	chr12:42469400-42491800	Weak transcription	Ovary	ovary
4	chr12:42470400-42479200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr12:42470400-42484000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:42470600-42484000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr12:42470600-42491400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr12:42470800-42480000	Weak transcription	A549	lung
9	chr12:42470800-42485600	Weak transcription	Aorta	Aorta
10	chr12:42471000-42504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:42471200-42479000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:42471200-42483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr12:42471400-42485600	Weak transcription	Fetal Muscle Leg	muscle
14	chr12:42471800-42483400	Weak transcription	Fetal Stomach	stomach
15	chr12:42471800-42486600	Weak transcription	Fetal Intestine Small	intestine
16	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
17	chr12:42472200-42487800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr12:42472800-42489000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr12:42473400-42480200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:42473600-42479200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:42473600-42481000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:42473600-42483600	Weak transcription	Adipose Nuclei	Adipose
23	chr12:42473600-42484000	Weak transcription	HUVEC	blood vessel
24	chr12:42473600-42484200	Weak transcription	Primary T cells from cord blood	blood
25	chr12:42473800-42484000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:42474000-42479000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr12:42474000-42479400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:42474000-42484000	Weak transcription	NH-A	brain
29	chr12:42474000-42484200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:42474000-42496000	Weak transcription	Fetal Intestine Large	intestine
31	chr12:42474200-42479600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr12:42474200-42484000	Weak transcription	Osteobl	bone
33	chr12:42474200-42486000	Weak transcription	GM12878-XiMat	blood
34	chr12:42474200-42487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:42474200-42490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:42474400-42480400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr12:42474600-42479400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr12:42474600-42479400	Weak transcription	Dnd41	blood
39	chr12:42474600-42479800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:42474600-42480600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr12:42474600-42482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
44	chr12:42474800-42487600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr12:42474800-42487600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr12:42474800-42491800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:42475000-42484200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:42475000-42491800	Weak transcription	Brain Substantia Nigra	brain
49	chr12:42475400-42485600	Weak transcription	Left Ventricle	heart
50	chr12:42475600-42479400	Weak transcription	Monocytes-CD14+_RO01746	blood

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