Variant report

Variant	rs151400
Chromosome Location	chr4:103187612-103187613
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:102265718..102267485-chr4:103187307..103189886,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs151368	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151369	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151372	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151388	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151392	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151393	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151394	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151395	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151396	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151397	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs151398	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs151399	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs151402	0.86[ASN][1000 genomes]
rs151403	0.86[ASN][1000 genomes]
rs17032416	0.85[AFR][1000 genomes]
rs189215	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs233824	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs233826	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs233831	0.84[ASN][1000 genomes]
rs233833	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs233834	0.85[ASN][1000 genomes]
rs367659	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs426642	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs439757	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs450780	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs456877	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs458318	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs458771	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs458779	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs460670	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs460800	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs462060	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs462178	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs463373	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs463661	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs464114	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs464969	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698843	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57957741	0.81[ASN][1000 genomes]
rs651551	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657521	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs657581	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6832846	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs685213	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9331	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9705	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv428447	chr4:103103730-103262107	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008680	chr4:103153709-103206555	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1011868	chr4:103158581-103206555	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999012	chr4:103162076-103206555	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1012254	chr4:103174196-103191787	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1014733	chr4:103174196-103206240	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1002129	chr4:103174196-103206555	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1013313	chr4:103175700-103206555	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1013439	chr4:103178743-103191787	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1003825	chr4:103179197-103206555	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv998689	chr4:103179788-103206555	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs151400	SLC39A8	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103179200-103202200	Weak transcription	Lung	lung
2	chr4:103179400-103188800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:103179400-103221000	Weak transcription	K562	blood
4	chr4:103180400-103200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:103181000-103188200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:103181400-103197600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:103181600-103210800	Weak transcription	Liver	Liver
8	chr4:103181800-103230400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:103182000-103255400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:103182800-103188200	Weak transcription	Placenta	Placenta
11	chr4:103183400-103210600	Weak transcription	Primary B cells from cord blood	blood
12	chr4:103184000-103196600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:103184200-103189200	Weak transcription	A549	lung
14	chr4:103184200-103220600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:103184400-103189200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:103184400-103190200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr4:103184600-103188200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr4:103184600-103188200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr4:103184600-103200400	Weak transcription	GM12878-XiMat	blood
20	chr4:103184600-103201000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:103185400-103189200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr4:103185600-103189200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:103185800-103188200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr4:103185800-103188400	Weak transcription	Primary T cells from cord blood	blood
25	chr4:103186600-103195400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:103186600-103229600	Weak transcription	Pancreas	Pancrea
27	chr4:103186800-103216800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr4:103187200-103188600	Weak transcription	Dnd41	blood
29	chr4:103187200-103200400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:103187200-103229400	Weak transcription	Fetal Thymus	thymus
31	chr4:103187600-103188400	Strong transcription	Hela-S3	cervix
32	chr4:103187600-103189600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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