Variant report

Variant	rs3886875
Chromosome Location	chr3:52454262-52454263
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	chr3:52452815..52455679-chr3:52718724..52720785,2	MCF-7	breast:
2	chr3:52445710..52451315-chr3:52451741..52455746,7	K562	blood:

Variant related genes	Relation type
ENSG00000163938	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10460962	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10461027	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10461028	0.86[EUR][1000 genomes]
rs10865971	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs11706515	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11706541	0.82[EUR][1000 genomes]
rs11707056	1.00[CEU][hapmap];0.88[GIH][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11708581	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11708811	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11710014	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs11711914	0.82[EUR][1000 genomes]
rs11711974	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11713914	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11714358	0.88[EUR][1000 genomes]
rs11715208	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11715391	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11716487	1.00[CEU][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs11717028	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11718729	0.84[EUR][1000 genomes]
rs11719760	0.82[EUR][1000 genomes]
rs11720365	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11721277	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052051	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17052052	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs17052053	0.91[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs17052054	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17263770	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1767	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1769	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs35976326	0.88[EUR][1000 genomes]
rs3733063	0.91[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs4082828	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs55676974	0.88[EUR][1000 genomes]
rs55724529	1.00[AFR][1000 genomes]
rs55806905	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55813842	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55847657	0.84[EUR][1000 genomes]
rs55946513	1.00[AFR][1000 genomes]
rs56002041	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56322342	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56352611	0.84[EUR][1000 genomes]
rs56366004	1.00[AFR][1000 genomes]
rs56899118	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57849650	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58531656	0.84[EUR][1000 genomes]
rs60382084	0.84[EUR][1000 genomes]
rs61644644	0.88[EUR][1000 genomes]
rs6445385	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6776759	0.92[EUR][1000 genomes]
rs6783652	0.88[EUR][1000 genomes]
rs6793317	0.91[CEU][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs6809248	0.84[EUR][1000 genomes]
rs724801	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs729555	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs73072990	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088773	0.85[EUR][1000 genomes]
rs73088783	0.84[EUR][1000 genomes]
rs73088785	0.84[EUR][1000 genomes]
rs73088791	0.88[EUR][1000 genomes]
rs73088800	0.84[EUR][1000 genomes]
rs73088802	1.00[AFR][1000 genomes]
rs73091166	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73091168	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs746239	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7615405	0.91[EUR][1000 genomes]
rs7628461	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs7633687	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7638204	1.00[CEU][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7643913	0.86[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
3	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
4	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3886875	SEMA3G	cis	cerebellum	SCAN
rs3886875	DNAH1	cis	cerebellum	SCAN
rs3886875	DNAH1	cis	parietal	SCAN
rs3886875	PPM1M	cis	parietal	SCAN
rs3886875	LOC286359	trans	parietal	SCAN
rs3886875	TKT	cis	cerebellum	SCAN
rs3886875	NISCH	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52445600-52471600	Weak transcription	Gastric	stomach
2	chr3:52445800-52456800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52445800-52457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:52445800-52457600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr3:52446200-52457400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:52446200-52463000	Weak transcription	Lung	lung
7	chr3:52446200-52465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:52446200-52467800	Weak transcription	Esophagus	oesophagus
9	chr3:52446400-52470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:52446600-52454800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:52446600-52455000	Weak transcription	Fetal Stomach	stomach
12	chr3:52446600-52455800	Weak transcription	Fetal Brain Female	brain
13	chr3:52446600-52457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:52446800-52455600	Weak transcription	Brain Substantia Nigra	brain
15	chr3:52446800-52456000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:52446800-52457200	Weak transcription	Primary B cells from cord blood	blood
17	chr3:52446800-52457200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:52446800-52457400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:52446800-52458200	Weak transcription	HepG2	liver
20	chr3:52446800-52460000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:52446800-52462400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:52446800-52463000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:52446800-52466000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:52447000-52456600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:52447000-52462800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:52447000-52464000	Weak transcription	Osteobl	bone
27	chr3:52447000-52470200	Weak transcription	Fetal Lung	lung
28	chr3:52447200-52454800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:52447200-52455400	Weak transcription	K562	blood
30	chr3:52447200-52456000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:52447200-52456400	Weak transcription	Brain Hippocampus Middle	brain
32	chr3:52447200-52456800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:52447200-52459000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:52447200-52461400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr3:52447200-52462400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:52447200-52462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:52447200-52462800	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:52447200-52463000	Weak transcription	Left Ventricle	heart
39	chr3:52447200-52463000	Weak transcription	Right Ventricle	heart
40	chr3:52447200-52468000	Weak transcription	Colonic Mucosa	Colon
41	chr3:52447400-52454400	Weak transcription	Primary T cells from cord blood	blood
42	chr3:52447400-52454600	Weak transcription	Brain Anterior Caudate	brain
43	chr3:52447400-52454600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr3:52447400-52455000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr3:52447400-52462800	Weak transcription	Brain Angular Gyrus	brain
46	chr3:52447400-52466200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:52447400-52467600	Weak transcription	NHEK	skin
48	chr3:52447600-52455800	Weak transcription	Fetal Heart	heart
49	chr3:52448200-52455000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:52448200-52463000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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