Variant report

Variant	rs3846488
Chromosome Location	chr5:52404287-52404288
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr5:52404015-52404311	K562	blood:	n/a	chr5:52404260-52404274 chr5:52404258-52404275 chr5:52404253-52404273
2	STAT1	chr5:52404264-52404456	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:52384729..52387843-chr5:52404184..52407459,4	MCF-7	breast:
2	chr5:52282064..52285632-chr5:52404082..52406997,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247796	TF binding region
MOCS2	TF binding region
ENSG00000164171	Chromatin interaction
ENSG00000272123	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10044163	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10045657	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10052267	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10064796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10072821	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471372	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10471831	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10471832	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16880890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16880902	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052567	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2062562	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28841614	0.89[AFR][1000 genomes]
rs28861745	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28890193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4555727	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9292008	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9292009	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
2	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:52392000-52404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:52392400-52404800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:52393000-52405000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:52393800-52404800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:52395400-52404800	Weak transcription	Aorta	Aorta
11	chr5:52395400-52405200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr5:52395600-52404400	Weak transcription	Thymus	Thymus
13	chr5:52395600-52404600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:52395600-52404800	Weak transcription	Colonic Mucosa	Colon
15	chr5:52395600-52404800	Weak transcription	Esophagus	oesophagus
16	chr5:52395600-52404800	Weak transcription	Fetal Brain Male	brain
17	chr5:52395600-52404800	Weak transcription	Pancreas	Pancrea
18	chr5:52395600-52404800	Weak transcription	Right Ventricle	heart
19	chr5:52395600-52405000	Weak transcription	Gastric	stomach
20	chr5:52395600-52405400	Weak transcription	Spleen	Spleen
21	chr5:52395800-52404600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr5:52395800-52404600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:52395800-52404800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:52395800-52405000	Weak transcription	Lung	lung
25	chr5:52395800-52405200	Weak transcription	Small Intestine	intestine
26	chr5:52396200-52404800	Weak transcription	Brain Angular Gyrus	brain
27	chr5:52396200-52404800	Weak transcription	Ovary	ovary
28	chr5:52396400-52404600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr5:52396400-52404800	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:52396600-52404400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr5:52396600-52404800	Weak transcription	Brain Substantia Nigra	brain
32	chr5:52397200-52404400	Weak transcription	Brain Anterior Caudate	brain
33	chr5:52397400-52404400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:52397400-52404600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:52397400-52404600	Weak transcription	Colon Smooth Muscle	Colon
36	chr5:52398000-52404600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:52398000-52404600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:52398000-52404800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr5:52399000-52404800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr5:52399600-52404800	Weak transcription	HSMMtube	muscle
41	chr5:52399600-52404800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:52399800-52404400	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr5:52399800-52404400	Weak transcription	Psoas Muscle	Psoas
44	chr5:52399800-52404600	Weak transcription	Fetal Stomach	stomach
45	chr5:52400000-52404400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:52400000-52404400	Weak transcription	Fetal Brain Female	brain
47	chr5:52400000-52404800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:52400000-52404800	Weak transcription	Fetal Intestine Small	intestine
49	chr5:52400200-52404600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:52400200-52404800	Weak transcription	Placenta	Placenta

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