Variant report

Variant	rs9650002
Chromosome Location	chr8:103307533-103307534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:103307488-103307734	MCF-7	breast:	n/a	n/a
2	POLR2A	chr8:103306946-103307735	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:103298397..103300610-chr8:103306655..103309037,2	MCF-7	breast:
2	chr8:103250799..103252817-chr8:103305128..103307836,2	MCF-7	breast:
3	chr8:103307064..103308726-chr8:103589205..103591686,2	MCF-7	breast:
4	chr8:103272916..103274548-chr8:103306550..103308849,2	MCF-7	breast:
5	chr8:103250313..103253012-chr8:103307347..103308859,2	K562	blood:
6	chr8:103306340..103308594-chr8:103820369..103822986,2	MCF-7	breast:
7	chr8:102445404..102448201-chr8:103307116..103309907,2	K562	blood:

No data

Variant related genes	Relation type
UBR5	TF binding region
ENSG00000048392	Chromatin interaction
ENSG00000104517	Chromatin interaction
ENSG00000246263	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10090707	1.00[MEX][hapmap]
rs10505020	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12707772	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs13248603	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13249865	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13250998	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13259151	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13261528	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13262662	0.95[EUR][1000 genomes]
rs13263132	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13269273	0.80[CEU][hapmap]
rs13269311	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13270908	0.98[EUR][1000 genomes]
rs13278798	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs13278875	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061299	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28927991	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28999669	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34270914	0.92[EUR][1000 genomes]
rs34278087	0.92[EUR][1000 genomes]
rs34279135	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34297513	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34351006	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34356268	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34730203	0.98[EUR][1000 genomes]
rs34976508	0.92[EUR][1000 genomes]
rs35166521	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35316247	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35558370	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35818724	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35873559	0.96[EUR][1000 genomes]
rs35969173	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35980679	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36178006	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4483125	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56003023	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572423	1.00[EUR][1000 genomes]
rs6468822	1.00[YRI][hapmap]
rs71518852	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71518861	0.87[EUR][1000 genomes]
rs71518862	0.90[EUR][1000 genomes]
rs7845877	0.88[EUR][1000 genomes]
rs9650000	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650001	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9650002	RIMS2	cis	cerebellum	SCAN
rs9650002	KCNS2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103252200-103318800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:103262600-103329800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr8:103263400-103327800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:103263400-103327800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr8:103266800-103329000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr8:103267400-103327800	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr8:103267400-103329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr8:103267600-103327800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr8:103268000-103327200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr8:103268200-103327600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr8:103268200-103328000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr8:103268800-103308400	Strong transcription	Fetal Muscle Leg	muscle
13	chr8:103287800-103312800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr8:103293800-103329200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr8:103296000-103312600	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr8:103296600-103327000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr8:103296800-103311400	Strong transcription	HUVEC	blood vessel
18	chr8:103297000-103312600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr8:103297000-103315400	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr8:103299800-103327600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr8:103299800-103329200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr8:103299800-103329200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr8:103300000-103312800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr8:103300000-103312800	Strong transcription	Fetal Intestine Large	intestine
25	chr8:103300000-103312800	Strong transcription	Fetal Thymus	thymus
26	chr8:103300000-103312800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr8:103300000-103313800	Weak transcription	Brain Angular Gyrus	brain
28	chr8:103300000-103326200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr8:103300000-103327200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr8:103300000-103328200	Strong transcription	HSMM	muscle
31	chr8:103300000-103328600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:103300000-103329400	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr8:103300000-103329800	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr8:103300000-103330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr8:103300200-103308200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr8:103300200-103312800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr8:103300200-103327000	Strong transcription	Adipose Nuclei	Adipose
38	chr8:103300200-103342800	Weak transcription	Stomach Mucosa	stomach
39	chr8:103300200-103343000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr8:103300400-103326200	Strong transcription	Primary T cells from cord blood	blood
41	chr8:103300400-103327400	Strong transcription	Liver	Liver
42	chr8:103300400-103327600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr8:103300600-103331600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr8:103300800-103327200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr8:103300800-103327600	Strong transcription	Placenta	Placenta
46	chr8:103300800-103328200	Strong transcription	Dnd41	blood
47	chr8:103301000-103327400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:103301800-103326400	Strong transcription	Fetal Lung	lung
49	chr8:103301800-103327000	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr8:103301800-103327200	Strong transcription	NH-A	brain

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