Variant report

Variant	rs3212433
Chromosome Location	chr5:52337144-52337145
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	chr5:52285122..52287993-chr5:52333837..52337640,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164171	Chromatin interaction
ENSG00000249899	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10041086	0.87[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075614	0.91[ASN][1000 genomes]
rs2287950	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212430	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212435	0.93[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212436	1.00[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212446	0.91[ASN][1000 genomes]
rs3212483	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3212537	0.89[ASN][1000 genomes]
rs3212556	0.88[ASN][1000 genomes]
rs3212583	0.86[YRI][hapmap]
rs3776788	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3776789	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3797494	0.87[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3797497	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797500	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62357234	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv880425	chr5:52291279-52345868	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv881217	chr5:52334774-52341512	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3212433	MOCS2	cis	brain	BrainEAC
rs3212433	MOCS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52327800-52344200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
5	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
6	chr5:52331800-52337200	Enhancers	HUVEC	blood vessel
7	chr5:52333400-52341400	Strong transcription	HepG2	liver
8	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
10	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
12	chr5:52334400-52338000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:52334600-52337400	Weak transcription	Adipose Nuclei	Adipose
15	chr5:52334600-52343400	Weak transcription	Gastric	stomach
16	chr5:52334600-52348400	Weak transcription	Lung	lung
17	chr5:52334800-52343400	Weak transcription	Esophagus	oesophagus
18	chr5:52334800-52343800	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:52334800-52343800	Weak transcription	Pancreas	Pancrea
20	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
21	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
22	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:52335200-52337800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:52335800-52338200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:52336000-52337800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:52336400-52337600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr5:52336400-52338800	Strong transcription	HMEC	breast
28	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:52336600-52337400	Active TSS	Primary hematopoietic stem cells	blood
30	chr5:52336600-52337400	Genic enhancers	NHEK	skin
31	chr5:52336800-52337400	Enhancers	Hela-S3	cervix
32	chr5:52337000-52337200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr5:52337000-52337200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr5:52337000-52337200	Enhancers	A549	lung
35	chr5:52337000-52337200	Flanking Active TSS	NHLF	lung
36	chr5:52337000-52337200	Flanking Active TSS	Osteobl	bone
37	chr5:52337000-52337400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr5:52337000-52337400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr5:52337000-52337400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr5:52337000-52337400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:52337000-52337400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr5:52337000-52337400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr5:52337000-52337400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
44	chr5:52337000-52337400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:52337000-52337400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr5:52337000-52337400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:52337000-52337400	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr5:52337000-52337400	Active TSS	Duodenum Mucosa	Duodenum
49	chr5:52337000-52337400	Enhancers	Fetal Kidney	kidney
50	chr5:52337000-52337400	Flanking Active TSS	GM12878-XiMat	blood

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