Variant report

Variant	rs829612
Chromosome Location	chr2:30631087-30631088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30628448..30631665-chr2:30638243..30640996,3	K562	blood:
2	chr2:30623807..30625999-chr2:30630909..30632513,2	K562	blood:
3	chr2:30627344..30629722-chr2:30630917..30632644,2	K562	blood:
4	chr2:30629437..30632185-chr2:30668589..30671116,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10495775	0.83[AFR][1000 genomes]
rs10514770	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11127273	0.82[EUR][1000 genomes]
rs1252616	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252617	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1252618	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12993465	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13000021	0.82[EUR][1000 genomes]
rs13012193	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13033921	0.82[EUR][1000 genomes]
rs2030744	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35909231	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4519571	0.81[EUR][1000 genomes]
rs6548013	0.82[EUR][1000 genomes]
rs7572690	0.89[CEU][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes]
rs7583194	0.84[EUR][1000 genomes]
rs7583844	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7593766	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829588	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829590	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs829609	0.82[AFR][1000 genomes]
rs829610	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]
rs829611	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829614	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917125	0.83[AFR][1000 genomes];0.96[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs829612	PREB	cis	parietal	SCAN
rs829612	DAB2IP	trans	cerebellum	SCAN
rs829612	FAM179A	cis	cerebellum	SCAN

Chromatin state (count:78 , 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	chr2:30628600-30631200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:30628600-30632800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:30628600-30634800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:30629400-30632000	Enhancers	Adipose Nuclei	Adipose
17	chr2:30629400-30632400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:30629400-30634200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:30629400-30635400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:30629600-30638000	Enhancers	Fetal Lung	lung
21	chr2:30629800-30634000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:30629800-30634200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr2:30629800-30638800	Enhancers	NHDF-Ad	bronchial
24	chr2:30630200-30631400	Enhancers	Fetal Intestine Large	intestine
25	chr2:30630200-30632200	Enhancers	HSMMtube	muscle
26	chr2:30630200-30632400	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr2:30630200-30633800	Enhancers	Ovary	ovary
28	chr2:30630200-30635200	Enhancers	Fetal Thymus	thymus
29	chr2:30630200-30638000	Enhancers	NHLF	lung
30	chr2:30630400-30631200	Enhancers	H1 Cell Line	embryonic stem cell
31	chr2:30630400-30631400	Enhancers	Aorta	Aorta
32	chr2:30630400-30631600	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr2:30630400-30631600	Enhancers	Fetal Muscle Trunk	muscle
34	chr2:30630400-30631600	Enhancers	Small Intestine	intestine
35	chr2:30630400-30631800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:30630400-30631800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:30630400-30631800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:30630400-30631800	Enhancers	Lung	lung
39	chr2:30630400-30632200	Enhancers	Right Atrium	heart
40	chr2:30630400-30632600	Enhancers	Fetal Muscle Leg	muscle
41	chr2:30630400-30632600	Enhancers	Placenta	Placenta
42	chr2:30630400-30632600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr2:30630400-30632600	Enhancers	HSMM	muscle
44	chr2:30630400-30632800	Enhancers	Spleen	Spleen
45	chr2:30630400-30633600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:30630400-30633800	Enhancers	Osteobl	bone
47	chr2:30630400-30634000	Enhancers	NH-A	brain
48	chr2:30630400-30634200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr2:30630400-30634200	Enhancers	Thymus	Thymus
50	chr2:30630400-30634200	Enhancers	HUVEC	blood vessel

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