Variant report

Variant	rs16833669
Chromosome Location	chr1:151920539-151920540
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151920501..151922320-chr1:151962400..151965015,2	MCF-7	breast:
2	chr1:151919533..151922319-chr1:151932817..151935606,2	MCF-7	breast:
3	chr1:151915835..151920651-chr1:152004121..152010886,7	MCF-7	breast:
4	chr1:151918309..151920987-chr1:151938809..151942058,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10494270	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204906	0.85[AMR][1000 genomes]
rs11204919	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204920	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11582739	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12083193	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12095483	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566232	0.82[AMR][1000 genomes]
rs16833668	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833670	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16833728	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16833743	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1844543	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2337685	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337686	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2338206	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28415528	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2932580	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34251437	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3791153	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4845719	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56000812	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56028913	0.80[AMR][1000 genomes]
rs56078223	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56170235	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56313205	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57674198	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57785325	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58087484	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61814883	0.85[ASN][1000 genomes]
rs61817695	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61817697	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61817719	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817720	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61817722	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817723	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61817724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61817725	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587632	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587633	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587634	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587635	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587636	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587637	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587638	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587640	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6657658	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6659662	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6662602	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662611	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6662728	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663064	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672064	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6675930	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678672	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6682605	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684114	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684312	0.87[AMR][1000 genomes]
rs6686874	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690449	0.87[AMR][1000 genomes]
rs6691212	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6693388	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693396	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6693901	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695324	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701374	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6703448	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6703465	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72694840	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7535002	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538652	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7541099	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554832	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7554859	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs902313	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971887	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9943221	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9943251	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16833669	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs16833669	THEM4	cis	multi-tissue	Pritchard
rs16833669	S100A10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151914000-151922000	Weak transcription	Spleen	Spleen
2	chr1:151916800-151920600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:151917600-151921800	Weak transcription	Lung	lung
4	chr1:151917600-151921800	Weak transcription	Pancreas	Pancrea
5	chr1:151918800-151925400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:151919000-151921800	Weak transcription	Ovary	ovary
7	chr1:151919200-151920600	Enhancers	HMEC	breast
8	chr1:151919200-151922000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:151919400-151921000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:151919400-151921200	Weak transcription	Adipose Nuclei	Adipose
11	chr1:151919600-151920800	Weak transcription	Esophagus	oesophagus
12	chr1:151919600-151921400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:151919600-151921400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:151919600-151921800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:151919600-151921800	Enhancers	Hela-S3	cervix
16	chr1:151919600-151922200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:151919600-151922800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:151919600-151924800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:151919800-151921000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:151919800-151921400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr1:151919800-151921800	Weak transcription	HSMM	muscle
22	chr1:151919800-151922600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:151919800-151925800	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:151920000-151921200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:151920000-151921600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr1:151920000-151925000	Weak transcription	A549	lung
27	chr1:151920400-151922600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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