Variant report

Variant	rs829610
Chromosome Location	chr2:30631693-30631694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30623807..30625999-chr2:30630909..30632513,2	K562	blood:
2	chr2:30627344..30629722-chr2:30630917..30632644,2	K562	blood:
3	chr2:30629437..30632185-chr2:30668589..30671116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10514770	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127273	0.81[EUR][1000 genomes]
rs1252616	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252617	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252618	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12993465	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13000021	0.81[EUR][1000 genomes]
rs13012193	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13033921	0.81[EUR][1000 genomes]
rs2030744	0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35909231	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4519571	0.80[EUR][1000 genomes]
rs6548013	0.81[EUR][1000 genomes]
rs7572690	0.85[CEU][hapmap];0.91[GIH][hapmap];0.81[EUR][1000 genomes]
rs7583194	0.83[EUR][1000 genomes]
rs7583844	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7593766	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829588	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829590	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs829611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829612	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829614	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917125	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv581262	chr2:30623062-30633796	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs829610	FAM179A	cis	cerebellum	SCAN
rs829610	PREB	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30619400-30637200	Enhancers	Fetal Stomach	stomach
2	chr2:30624800-30633200	Enhancers	Fetal Heart	heart
3	chr2:30625000-30636200	Enhancers	Rectal Smooth Muscle	rectum
4	chr2:30626000-30633800	Enhancers	Left Ventricle	heart
5	chr2:30626000-30634000	Enhancers	Right Ventricle	heart
6	chr2:30626000-30638000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:30627600-30647200	Weak transcription	Brain Angular Gyrus	brain
8	chr2:30628000-30644400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:30628200-30633400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:30628200-30636000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:30628400-30632800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:30628400-30639800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:30628600-30632800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:30628600-30634800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:30629400-30632000	Enhancers	Adipose Nuclei	Adipose
16	chr2:30629400-30632400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:30629400-30634200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:30629400-30635400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:30629600-30638000	Enhancers	Fetal Lung	lung
20	chr2:30629800-30634000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:30629800-30634200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:30629800-30638800	Enhancers	NHDF-Ad	bronchial
23	chr2:30630200-30632200	Enhancers	HSMMtube	muscle
24	chr2:30630200-30632400	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr2:30630200-30633800	Enhancers	Ovary	ovary
26	chr2:30630200-30635200	Enhancers	Fetal Thymus	thymus
27	chr2:30630200-30638000	Enhancers	NHLF	lung
28	chr2:30630400-30631800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:30630400-30631800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:30630400-30631800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:30630400-30631800	Enhancers	Lung	lung
32	chr2:30630400-30632200	Enhancers	Right Atrium	heart
33	chr2:30630400-30632600	Enhancers	Fetal Muscle Leg	muscle
34	chr2:30630400-30632600	Enhancers	Placenta	Placenta
35	chr2:30630400-30632600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr2:30630400-30632600	Enhancers	HSMM	muscle
37	chr2:30630400-30632800	Enhancers	Spleen	Spleen
38	chr2:30630400-30633600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:30630400-30633800	Enhancers	Osteobl	bone
40	chr2:30630400-30634000	Enhancers	NH-A	brain
41	chr2:30630400-30634200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:30630400-30634200	Enhancers	Thymus	Thymus
43	chr2:30630400-30634200	Enhancers	HUVEC	blood vessel
44	chr2:30630600-30631800	Enhancers	Primary B cells from peripheral blood	blood
45	chr2:30630600-30631800	Enhancers	Fetal Intestine Small	intestine
46	chr2:30630600-30632000	Enhancers	Muscle Satellite Cultured Cells	--
47	chr2:30630600-30632000	Enhancers	Fetal Kidney	kidney
48	chr2:30630600-30635000	Enhancers	Primary T cells from cord blood	blood
49	chr2:30630800-30632000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:30630800-30632200	Enhancers	Rectal Mucosa Donor 29	rectum

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