Variant report

Variant	rs7621415
Chromosome Location	chr3:155476547-155476548
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155468097..155470070-chr3:155473602..155476572,2	K562	blood:
2	chr3:155475971..155478376-chr3:155587732..155590081,2	K562	blood:

Variant related genes	Relation type
ENSG00000163655	Chromatin interaction

Extended variants
information (count: 37 )
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]
rs7615938	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]
rs7617878	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:6 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7621415	RARRES1	cis	cerebellum	SCAN
rs7621415	SLC33A1	cis	parietal	SCAN
rs7621415	SLC33A1	cis	cerebellum	SCAN

Chromatin state (count:52 , 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	chr3:155464000-155476600	Weak transcription	Ovary	ovary
4	chr3:155464200-155487600	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:155464200-155487600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:155464200-155487800	Weak transcription	Adipose Nuclei	Adipose
7	chr3:155464200-155487800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:155464200-155487800	Weak transcription	Pancreas	Pancrea
9	chr3:155464200-155489600	Weak transcription	Brain Anterior Caudate	brain
10	chr3:155464200-155490600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:155464600-155487800	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:155466400-155484600	Weak transcription	Fetal Brain Male	brain
13	chr3:155467000-155487200	Weak transcription	Fetal Brain Female	brain
14	chr3:155467200-155478400	Weak transcription	Fetal Intestine Large	intestine
15	chr3:155467200-155479400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:155467200-155500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:155467200-155508000	Weak transcription	K562	blood
18	chr3:155467200-155508800	Weak transcription	Hela-S3	cervix
19	chr3:155467400-155481600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:155467400-155508400	Weak transcription	HepG2	liver
21	chr3:155468000-155487200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:155469400-155481600	Weak transcription	Liver	Liver
23	chr3:155470000-155478800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:155470200-155483000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:155470400-155487400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:155470400-155487600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:155470800-155487400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:155471000-155481400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:155471000-155487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:155471000-155487800	Weak transcription	Right Ventricle	heart
31	chr3:155471200-155487600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:155471400-155509000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:155471800-155487600	Weak transcription	Brain Angular Gyrus	brain
34	chr3:155472200-155487600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:155472400-155487200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:155472800-155488000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:155472800-155500000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:155473200-155487400	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:155473200-155487400	Weak transcription	Thymus	Thymus
40	chr3:155474200-155487600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:155474200-155487800	Weak transcription	Spleen	Spleen
42	chr3:155474200-155490600	Weak transcription	Colon Smooth Muscle	Colon
43	chr3:155474200-155497600	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:155474400-155492000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr3:155474800-155476600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:155474800-155487400	Weak transcription	Dnd41	blood
47	chr3:155474800-155487800	Weak transcription	Primary T cells from cord blood	blood
48	chr3:155474800-155489000	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:155475200-155491000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:155475200-155492200	Weak transcription	Fetal Kidney	kidney

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