Variant report

Variant	rs7615938
Chromosome Location	chr3:155484317-155484318
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:155479593..155481988-chr3:155483221..155485642,3	K562	blood:
2	chr3:155483233..155486124-chr3:155587848..155589390,2	MCF-7	breast:
3	chr3:155481429..155485286-chr3:155486373..155491702,5	K562	blood:

Variant related genes	Relation type
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs17349490	0.82[GIH][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes]
rs17349560	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415195	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17415343	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56213840	1.00[ASN][1000 genomes]
rs57149264	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58227176	1.00[ASN][1000 genomes]
rs6765861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782387	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156584	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156593	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156600	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73156602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159011	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159017	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159021	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159025	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159026	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159032	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159054	1.00[ASN][1000 genomes]
rs73159063	1.00[ASN][1000 genomes]
rs73159074	1.00[ASN][1000 genomes]
rs73873405	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615287	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7617878	1.00[ASN][1000 genomes]
rs7621415	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641701	1.00[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648978	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757945	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882341	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009618	chr3:155370034-155492177	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	nsv592079	chr3:155474879-155493915	Strong transcription ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1009635	chr3:155475438-155515484	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010726	chr3:155476547-155492177	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1007915	chr3:155476547-155513397	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv592080	chr3:155479222-155511844	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	esv14416	chr3:155479247-155512774	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv514997	chr3:155481066-155491738	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv441844	chr3:155481096-155492177	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv2763741	chr3:155481097-155492177	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1004723	chr3:155481097-155492177	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv592081	chr3:155481097-155493915	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv592082	chr3:155481097-155500859	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv1006439	chr3:155481097-155515484	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	nsv1014031	chr3:155481097-155524777	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv999641	chr3:155481097-155534616	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	esv33346	chr3:155481220-155498441	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
19	esv3693343	chr3:155481609-155493915	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv516712	chr3:155481609-155493915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv818180	chr3:155481609-155493915	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv592083	chr3:155484125-155498311	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
23	nsv963538	chr3:155484316-155497006	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7615938	SLC33A1	cis	cerebellum	SCAN
rs7615938	SLC33A1	cis	parietal	SCAN
rs7615938	RARRES1	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155463800-155487800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:155463800-155501200	Weak transcription	Aorta	Aorta
3	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
6	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
8	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
9	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:155466400-155484600	Weak transcription	Fetal Brain Male	brain
12	chr3:155467000-155487200	Weak transcription	Fetal Brain Female	brain
13	chr3:155467200-155500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:155467200-155508000	Weak transcription	K562	blood
15	chr3:155467200-155508800	Weak transcription	Hela-S3	cervix
16	chr3:155467400-155508400	Weak transcription	HepG2	liver
17	chr3:155468000-155487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:155470400-155487400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:155470400-155487600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:155470800-155487400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:155471000-155487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:155471000-155487800	Weak transcription	Right Ventricle	heart
23	chr3:155471200-155487600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:155471400-155509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:155471800-155487600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:155472200-155487600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:155472400-155487200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:155472800-155488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:155472800-155500000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:155473200-155487400	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:155473200-155487400	Weak transcription	Thymus	Thymus
32	chr3:155474200-155487600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:155474200-155487800	Weak transcription	Spleen	Spleen
34	chr3:155474200-155490600	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:155474200-155497600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:155474400-155492000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr3:155474800-155487400	Weak transcription	Dnd41	blood
38	chr3:155474800-155487800	Weak transcription	Primary T cells from cord blood	blood
39	chr3:155474800-155489000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:155475200-155491000	Weak transcription	Rectal Smooth Muscle	rectum
41	chr3:155475200-155492200	Weak transcription	Fetal Kidney	kidney
42	chr3:155476400-155487400	Weak transcription	Left Ventricle	heart
43	chr3:155476400-155487800	Weak transcription	Fetal Stomach	stomach
44	chr3:155476600-155500000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:155477000-155487600	Weak transcription	Ovary	ovary
46	chr3:155478400-155487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:155478400-155487400	Weak transcription	Brain Germinal Matrix	brain
48	chr3:155478600-155509000	Weak transcription	Gastric	stomach
49	chr3:155478800-155487400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:155478800-155487800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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