Variant report

Variant	rs10029785
Chromosome Location	chr4:48346993-48346994
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48270465..48272288-chr4:48345369..48347780,2	MCF-7	breast:
2	chr4:48341581..48344339-chr4:48345461..48347576,2	MCF-7	breast:
3	chr4:48346882..48348699-chr4:48349922..48352007,2	K562	blood:

Variant related genes	Relation type
ENSG00000135605	Chromatin interaction
ENSG00000109171	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10003230	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10026398	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10938534	0.81[JPT][hapmap]
rs11945562	0.86[JPT][hapmap]
rs12645501	0.81[JPT][hapmap]
rs12645951	0.89[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13105385	0.81[AFR][1000 genomes]
rs1352433	0.82[AFR][1000 genomes]
rs1472967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1703973	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2029348	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291474	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2291475	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2353312	0.83[ASN][1000 genomes]
rs372825	0.85[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs382335	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3828496	0.82[AFR][1000 genomes]
rs392187	0.83[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs403495	0.84[ASN][1000 genomes]
rs404348	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs404445	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs404656	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs411261	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs421336	0.91[ASN][1000 genomes]
rs421833	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs429969	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs432927	0.91[ASN][1000 genomes]
rs445892	0.87[ASN][1000 genomes]
rs449376	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs450498	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62309425	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6447635	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6811148	0.81[JPT][hapmap]
rs6816010	0.89[ASW][hapmap];0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6816352	0.83[ASN][1000 genomes]
rs6821277	0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[ASN][1000 genomes]
rs6829705	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6829716	0.86[JPT][hapmap]
rs6836010	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6836632	0.86[JPT][hapmap]
rs6837335	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6844211	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6848073	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6848395	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7438704	0.89[ASW][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.83[MKK][hapmap];0.84[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7654770	0.86[JPT][hapmap]
rs7668529	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7672892	0.82[AFR][1000 genomes]
rs7678164	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7678379	0.86[JPT][hapmap]
rs7683398	0.81[JPT][hapmap]
rs7697851	0.86[JPT][hapmap]
rs7700018	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs937888	0.81[JPT][hapmap]
rs992423	0.86[JPT][hapmap]
rs9996532	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006610	chr4:48209294-48415387	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv537085	chr4:48209294-48415387	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10029785	OCIAD2	cis	cerebellum	SCAN
rs10029785	SLAIN2	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48344600-48347200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:48344800-48347000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:48344800-48347000	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr4:48344800-48349000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:48344800-48349200	Weak transcription	Lung	lung
6	chr4:48344800-48352200	Weak transcription	Pancreas	Pancrea
7	chr4:48344800-48354400	Weak transcription	Esophagus	oesophagus
8	chr4:48344800-48362400	Weak transcription	Gastric	stomach
9	chr4:48345000-48347400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr4:48345000-48350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr4:48345200-48349200	Weak transcription	Left Ventricle	heart
12	chr4:48345400-48347200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:48345400-48347200	Enhancers	Fetal Stomach	stomach
14	chr4:48345400-48347400	Enhancers	Brain Cingulate Gyrus	brain
15	chr4:48345400-48347600	Enhancers	Liver	Liver
16	chr4:48345400-48350400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:48345600-48347000	Flanking Active TSS	K562	blood
18	chr4:48345600-48347600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:48345600-48347600	Enhancers	Brain Hippocampus Middle	brain
20	chr4:48345600-48347600	Enhancers	Rectal Smooth Muscle	rectum
21	chr4:48345600-48349400	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr4:48345800-48347000	Enhancers	HSMM	muscle
23	chr4:48345800-48347400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:48345800-48347400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:48345800-48347400	Enhancers	Fetal Brain Male	brain
26	chr4:48345800-48347600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:48345800-48347600	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr4:48345800-48347600	Enhancers	Brain Angular Gyrus	brain
29	chr4:48345800-48347800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr4:48345800-48348600	Enhancers	Fetal Lung	lung
31	chr4:48345800-48348800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr4:48345800-48349200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr4:48345800-48349400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr4:48345800-48353600	Weak transcription	Spleen	Spleen
35	chr4:48345800-48356000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr4:48345800-48356600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:48346000-48347000	Enhancers	Aorta	Aorta
38	chr4:48346000-48347400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr4:48346000-48347600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr4:48346000-48347600	Enhancers	Fetal Heart	heart
41	chr4:48346000-48348200	Weak transcription	HSMMtube	muscle
42	chr4:48346000-48348600	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr4:48346000-48348600	Enhancers	HepG2	liver
44	chr4:48346000-48348800	Active TSS	GM12878-XiMat	blood
45	chr4:48346000-48349200	Enhancers	Colon Smooth Muscle	Colon
46	chr4:48346000-48349400	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr4:48346000-48350000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr4:48346000-48350800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:48346000-48351200	Weak transcription	A549	lung
50	chr4:48346000-48353000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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