Variant report

Variant	rs2512411
Chromosome Location	chr8:103326735-103326736
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	chr8:103315506..103318243-chr8:103326156..103330411,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104517	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1265116	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1265118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs1265154	1.00[CHB][hapmap]
rs17435369	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17512088	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17526503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2045412	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2168690	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2445947	0.91[EUR][1000 genomes]
rs2512410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607661	0.82[CEU][hapmap];0.93[EUR][1000 genomes]
rs2853230	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2853235	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2925781	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2925790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2978431	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3018505	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3018508	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs58013140	0.92[AFR][1000 genomes]
rs58217487	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61149171	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62523108	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6988618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6996619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7840833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9773443	1.00[CHB][hapmap];0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv528486	chr8:103279922-103373304	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv891244	chr8:103309862-103483466	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2512411	RRM2B	cis	cerebellum	SCAN
rs2512411	KLF10	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103262600-103329800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr8:103263400-103327800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr8:103263400-103327800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:103266800-103329000	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr8:103267400-103327800	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr8:103267400-103329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr8:103267600-103327800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr8:103268000-103327200	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr8:103268200-103327600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:103268200-103328000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr8:103293800-103329200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:103296600-103327000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:103299800-103327600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr8:103299800-103329200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr8:103299800-103329200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr8:103300000-103327200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:103300000-103328200	Strong transcription	HSMM	muscle
18	chr8:103300000-103328600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr8:103300000-103329400	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr8:103300000-103329800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr8:103300000-103330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr8:103300200-103327000	Strong transcription	Adipose Nuclei	Adipose
23	chr8:103300200-103342800	Weak transcription	Stomach Mucosa	stomach
24	chr8:103300200-103343000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr8:103300400-103327400	Strong transcription	Liver	Liver
26	chr8:103300400-103327600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr8:103300600-103331600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr8:103300800-103327200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:103300800-103327600	Strong transcription	Placenta	Placenta
30	chr8:103300800-103328200	Strong transcription	Dnd41	blood
31	chr8:103301000-103327400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr8:103301800-103327000	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr8:103301800-103327200	Strong transcription	NH-A	brain
34	chr8:103301800-103327400	Strong transcription	K562	blood
35	chr8:103302600-103327200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr8:103303200-103327200	Strong transcription	Duodenum Mucosa	Duodenum
37	chr8:103303400-103327200	Strong transcription	Osteobl	bone
38	chr8:103303800-103327200	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr8:103304000-103328000	Strong transcription	Primary B cells from cord blood	blood
40	chr8:103304400-103328200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr8:103304600-103329400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr8:103304800-103326800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr8:103305000-103327000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr8:103306000-103327200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr8:103308000-103338200	Weak transcription	Gastric	stomach
46	chr8:103313400-103327200	Strong transcription	Fetal Muscle Leg	muscle
47	chr8:103313600-103327000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr8:103313600-103327000	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr8:103313600-103327200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr8:103313600-103327200	Strong transcription	Fetal Muscle Trunk	muscle

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