Variant report

Variant	rs7652005
Chromosome Location	chr3:155617205-155617206
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155602292..155604191-chr3:155617087..155618937,2	MCF-7	breast:
2	chr3:155608769..155610582-chr3:155616040..155618696,2	K562	blood:
3	chr3:155611421..155613972-chr3:155615607..155618374,3	K562	blood:

Variant related genes	Relation type
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10804773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10804774	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10936020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131925	0.91[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs11706359	0.92[CEU][hapmap]
rs11714133	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13059611	0.87[ASN][1000 genomes]
rs13091683	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13096499	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2054878	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2063903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2200707	0.81[CEU][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap]
rs34337666	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35321137	0.95[ASN][1000 genomes]
rs35472369	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs358703	0.87[ASW][hapmap];0.82[CEU][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap]
rs3772115	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772116	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821365	0.99[ASN][1000 genomes]
rs4680219	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680223	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55662848	0.81[EUR][1000 genomes]
rs6441028	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.99[ASN][1000 genomes]
rs66509404	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763830	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6799267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6804740	0.81[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6809229	0.87[ASW][hapmap];0.96[CEU][hapmap];0.86[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.80[EUR][1000 genomes]
rs7619976	0.97[ASN][1000 genomes]
rs7629523	0.80[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap]
rs7633168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7643630	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877680	chr3:155438022-155723064	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2753744	chr3:155487298-155707298	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv877681	chr3:155535670-155654017	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7652005	SLC33A1	cis	cerebellum	SCAN
rs7652005	RARRES1	cis	cerebellum	SCAN
rs7652005	SLC33A1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155590200-155643000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:155590200-155667400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:155594200-155622000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:155598600-155630000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:155599800-155633400	Weak transcription	Right Ventricle	heart
6	chr3:155603800-155657800	Weak transcription	Esophagus	oesophagus
7	chr3:155604400-155658600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:155605000-155632600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:155607000-155633400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:155607200-155656800	Weak transcription	Small Intestine	intestine
11	chr3:155607400-155625800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr3:155607400-155630600	Weak transcription	Lung	lung
13	chr3:155607400-155632600	Weak transcription	Gastric	stomach
14	chr3:155607400-155669000	Weak transcription	Pancreas	Pancrea
15	chr3:155607800-155625600	Weak transcription	Brain Germinal Matrix	brain
16	chr3:155608600-155646400	Strong transcription	Dnd41	blood
17	chr3:155608800-155630000	Weak transcription	Fetal Heart	heart
18	chr3:155608800-155632600	Weak transcription	Spleen	Spleen
19	chr3:155608800-155633400	Weak transcription	Psoas Muscle	Psoas
20	chr3:155608800-155633800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr3:155608800-155654800	Weak transcription	Aorta	Aorta
22	chr3:155609000-155630000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:155609000-155633800	Weak transcription	Stomach Mucosa	stomach
24	chr3:155609200-155622400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:155609200-155657200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:155609600-155652000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:155609800-155627400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:155610400-155631200	Strong transcription	K562	blood
29	chr3:155610600-155625600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:155610800-155621000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:155610800-155621000	Strong transcription	Hela-S3	cervix
32	chr3:155610800-155625600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:155610800-155625600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:155610800-155632600	Weak transcription	Colonic Mucosa	Colon
35	chr3:155610800-155638200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:155610800-155646200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:155610800-155646200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr3:155611000-155646200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:155611000-155646200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:155611200-155619200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:155611200-155619800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:155611200-155621600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:155611200-155625600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:155611200-155625800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:155611200-155631000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:155611200-155646200	Strong transcription	Fetal Thymus	thymus
47	chr3:155611400-155618000	Strong transcription	Fetal Intestine Large	intestine
48	chr3:155611400-155620400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:155611400-155625200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:155611400-155626000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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