Variant report

Variant	rs11149843
Chromosome Location	chr16:75649275-75649276
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:75634410..75636318-chr16:75647297..75649733,2	K562	blood:
2	chr16:75599248..75601815-chr16:75649137..75652321,3	MCF-7	breast:
3	chr16:75639999..75645390-chr16:75646099..75650752,7	K562	blood:
4	chr16:75628689..75631132-chr16:75648256..75650154,2	K562	blood:
5	chr16:75647375..75649764-chr16:75653227..75655141,2	K562	blood:
6	chr16:75649115..75650926-chr16:75653662..75655747,3	MCF-7	breast:
7	chr16:75648280..75653154-chr16:75655873..75659174,5	K562	blood:

Variant related genes	Relation type
ENSG00000065457	Chromatin interaction
ENSG00000034713	Chromatin interaction
ENSG00000259992	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10781978	0.87[ASN][1000 genomes]
rs12596662	0.88[ASN][1000 genomes]
rs1874022	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2550913	0.88[LWK][hapmap]
rs3743598	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3784929	0.87[GIH][hapmap]
rs3863448	0.90[CHD][hapmap];0.80[GIH][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];1.00[MKK][hapmap]
rs41505349	0.89[GIH][hapmap]
rs4888439	0.81[AFR][1000 genomes]
rs4888441	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5010692	0.87[GIH][hapmap]
rs55864135	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61310184	0.85[ASN][1000 genomes]
rs6564267	0.90[CHD][hapmap];0.85[GIH][hapmap]
rs7189895	0.90[CHD][hapmap];0.80[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.86[YRI][hapmap]
rs8048944	0.86[AFR][1000 genomes]
rs8060972	0.82[CHB][hapmap]
rs964632	0.81[GIH][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap];0.82[TSI][hapmap]
rs9934159	0.89[GIH][hapmap]

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	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11149843	ADAT1	cis	cerebellum	SCAN
rs11149843	ADAT1	cis	Adipose Subcutaneous	GTEx
rs11149843	ADAT1	cis	parietal	SCAN
rs11149843	ADAT1	cis	Artery Tibial	GTEx
rs11149843	ADAT1	cis	lung	GTEx
rs11149843	ADAT1	cis	Thyroid	GTEx
rs11149843	ADAT1	cis	Esophagus Mucosa	GTEx
rs11149843	ADAT1	cis	Nerve Tibial	GTEx
rs11149843	ADAT1	cis	multi-tissue	Pritchard
rs11149843	ADAT1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75629000-75650600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr16:75629600-75654800	Strong transcription	Fetal Stomach	stomach
3	chr16:75630600-75654600	Strong transcription	Fetal Intestine Large	intestine
4	chr16:75631000-75649400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr16:75631400-75654600	Strong transcription	Brain Hippocampus Middle	brain
6	chr16:75631400-75654600	Strong transcription	Fetal Muscle Leg	muscle
7	chr16:75631400-75655200	Strong transcription	Fetal Muscle Trunk	muscle
8	chr16:75632600-75654800	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr16:75633000-75654400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr16:75633000-75654400	Strong transcription	Fetal Thymus	thymus
11	chr16:75633200-75654800	Strong transcription	Liver	Liver
12	chr16:75633400-75653200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr16:75634400-75654600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr16:75634400-75654800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:75636200-75651200	Strong transcription	Hela-S3	cervix
16	chr16:75636400-75653800	Strong transcription	Placenta	Placenta
17	chr16:75636600-75653800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr16:75636600-75654200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr16:75636600-75654400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr16:75636600-75654400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr16:75636600-75654800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr16:75636800-75654200	Strong transcription	Fetal Brain Female	brain
23	chr16:75637000-75654400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr16:75637000-75654400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr16:75637000-75654600	Strong transcription	Primary T cells from cord blood	blood
26	chr16:75637000-75654600	Strong transcription	Fetal Intestine Small	intestine
27	chr16:75637200-75653400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr16:75637200-75654400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr16:75637400-75654600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr16:75637400-75654600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr16:75637400-75654800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr16:75637400-75655200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr16:75637800-75650400	Weak transcription	Fetal Brain Male	brain
34	chr16:75637800-75654800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr16:75637800-75655200	Weak transcription	Stomach Mucosa	stomach
36	chr16:75638000-75654000	Strong transcription	Dnd41	blood
37	chr16:75638000-75655000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr16:75638800-75654600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr16:75639200-75654400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr16:75639400-75654600	Strong transcription	Thymus	Thymus
41	chr16:75639400-75654800	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr16:75639800-75653600	Strong transcription	Primary hematopoietic stem cells	blood
43	chr16:75639800-75654600	Strong transcription	Brain Anterior Caudate	brain
44	chr16:75639800-75654800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr16:75640000-75649400	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr16:75640000-75654200	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr16:75640000-75654400	Strong transcription	Adipose Nuclei	Adipose
48	chr16:75640000-75654600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr16:75640200-75653600	Strong transcription	Brain Germinal Matrix	brain
50	chr16:75640200-75654600	Strong transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links