Variant report

Variant	rs2436929
Chromosome Location	chr8:103612708-103612709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:39)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:39 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:103611934..103614222-chr8:103799650..103801342,2	MCF-7	breast:
2	chr8:103612475..103613967-chr8:103822902..103824162,4	MCF-7	breast:
3	chr8:103611593..103614378-chr8:103673976..103676752,2	MCF-7	breast:
4	chr8:103611533..103613612-chr8:103826955..103829615,2	MCF-7	breast:
5	chr8:103597950..103598611-chr8:103612595..103613568,2	MCF-7	breast:
6	chr8:103605858..103620203-chr8:103816083..103827169,111	MCF-7	breast:
7	chr8:103612309..103614258-chr8:103757313..103760132,2	MCF-7	breast:
8	chr8:103612606..103614596-chr8:103644963..103646677,2	MCF-7	breast:
9	chr8:103413097..103415082-chr8:103611683..103614230,3	MCF-7	breast:
10	chr8:103539417..103541497-chr8:103612247..103613924,2	MCF-7	breast:
11	chr11:65188907..65191280-chr8:103610894..103613033,2	MCF-7	breast:
12	chr8:103611028..103613116-chr8:103635712..103638657,2	K562	blood:
13	chr8:103590076..103590706-chr8:103612649..103613335,2	MCF-7	breast:
14	chr8:103612111..103614488-chr8:103776554..103778954,2	MCF-7	breast:
15	chr8:103612415..103613811-chr8:103665804..103666814,6	MCF-7	breast:
16	chr1:247177709..247178479-chr8:103612663..103613495,2	MCF-7	breast:
17	chr8:103610682..103613281-chr8:103617723..103620341,2	K562	blood:
18	chr8:103610633..103618537-chr8:103662081..103669570,24	MCF-7	breast:
19	chr8:103588260..103591760-chr8:103612435..103616119,7	MCF-7	breast:
20	chr8:103610502..103616206-chr8:103792660..103796842,13	MCF-7	breast:
21	chr8:103612230..103614830-chr8:103769298..103771292,3	MCF-7	breast:
22	chr8:103606352..103608915-chr8:103612580..103614660,2	K562	blood:
23	chr8:103612630..103613493-chr8:103639463..103640288,2	MCF-7	breast:
24	chr8:103612224..103613922-chr8:103713851..103716447,2	MCF-7	breast:
25	chr8:103612523..103614553-chr8:103650121..103652108,2	MCF-7	breast:
26	chr8:103611190..103612835-chr8:103749951..103752657,2	MCF-7	breast:
27	chr8:103249747..103252065-chr8:103611727..103613272,2	MCF-7	breast:
28	chr8:103611183..103613432-chr8:103875344..103878248,3	MCF-7	breast:
29	chr8:103249682..103253435-chr8:103611734..103616089,6	MCF-7	breast:
30	chr8:103612415..103613811-chr8:103665750..103666814,7	MCF-7	breast:
31	chr8:103612597..103614487-chr8:103669576..103671484,2	MCF-7	breast:
32	chr8:103610542..103615201-chr8:103799392..103803025,12	MCF-7	breast:
33	chr8:103612611..103613494-chr8:103663794..103664718,2	MCF-7	breast:
34	chr8:103394320..103397702-chr8:103611755..103614575,3	MCF-7	breast:
35	chr8:103612645..103615158-chr8:103875756..103877314,2	MCF-7	breast:
36	chr8:103420304..103422038-chr8:103611446..103613008,2	MCF-7	breast:
37	chr8:103611739..103615321-chr8:103653896..103661701,12	MCF-7	breast:
38	chr8:103422529..103425503-chr8:103610947..103614616,5	MCF-7	breast:
39	chr8:103606751..103617128-chr8:103816392..103825354,41	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000048392	Chromatin interaction
ENSG00000246263	Chromatin interaction
ENSG00000236775	Chromatin interaction
ENSG00000155090	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000104517	Chromatin interaction
ENSG00000253633	Chromatin interaction
ENSG00000155096	Chromatin interaction
ENSG00000253669	Chromatin interaction
ENSG00000245532	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12543046	0.80[MEX][hapmap]
rs2436950	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511658	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2511675	0.90[CHB][hapmap]
rs2511676	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2511679	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33118	chr8:103358567-104068172	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1031769	chr8:103460754-103620283	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv539703	chr8:103460754-103620283	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv2762761	chr8:103492356-103625244	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1028329	chr8:103574775-103684362	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2436929	SPAG1	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103603800-103613000	Weak transcription	Right Atrium	heart
2	chr8:103605200-103612800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:103609800-103612800	Enhancers	K562	blood
4	chr8:103611000-103612800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr8:103611000-103612800	Weak transcription	Osteobl	bone
6	chr8:103611000-103613000	Weak transcription	Colon Smooth Muscle	Colon
7	chr8:103611400-103612800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr8:103611800-103612800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr8:103611800-103612800	Enhancers	Adipose Nuclei	Adipose
10	chr8:103611800-103612800	Bivalent Enhancer	Fetal Muscle Leg	muscle
11	chr8:103612000-103612800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr8:103612000-103612800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr8:103612000-103612800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:103612200-103612800	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr8:103612200-103612800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr8:103612200-103612800	Active TSS	Brain Substantia Nigra	brain
17	chr8:103612200-103612800	Enhancers	Placenta	Placenta
18	chr8:103612200-103612800	Enhancers	Left Ventricle	heart
19	chr8:103612200-103613000	Enhancers	Pancreas	Pancrea
20	chr8:103612200-103613000	Enhancers	Right Ventricle	heart
21	chr8:103612200-103613000	Flanking Active TSS	Hela-S3	cervix
22	chr8:103612200-103613800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr8:103612200-103614000	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr8:103612200-103614000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr8:103612200-103614200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr8:103612200-103614200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr8:103612400-103612800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr8:103612400-103612800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
29	chr8:103612400-103612800	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr8:103612400-103612800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr8:103612400-103612800	Enhancers	Colonic Mucosa	Colon
32	chr8:103612400-103612800	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr8:103612400-103612800	Enhancers	Fetal Intestine Large	intestine
34	chr8:103612400-103612800	Enhancers	Fetal Intestine Small	intestine
35	chr8:103612400-103612800	Bivalent Enhancer	Thymus	Thymus
36	chr8:103612400-103613000	Bivalent Enhancer	Primary B cells from cord blood	blood
37	chr8:103612400-103613000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr8:103612400-103613000	Enhancers	Esophagus	oesophagus
39	chr8:103612400-103613000	Enhancers	Fetal Heart	heart
40	chr8:103612400-103613000	Enhancers	Ovary	ovary
41	chr8:103612400-103613000	Enhancers	Psoas Muscle	Psoas
42	chr8:103612400-103613200	Flanking Active TSS	Liver	Liver
43	chr8:103612400-103613800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr8:103612400-103614000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr8:103612400-103614000	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr8:103612400-103614000	Enhancers	Gastric	stomach
47	chr8:103612400-103614000	Enhancers	Lung	lung
48	chr8:103612400-103614000	Enhancers	Spleen	Spleen
49	chr8:103612600-103612800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr8:103612600-103612800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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