Variant report

Variant	rs7895646
Chromosome Location	chr10:99167436-99167437
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99165865..99167587-chr10:99186226..99189247,3	MCF-7	breast:
2	chr10:99165782..99177128-chr10:99179856..99189832,30	MCF-7	breast:
3	chr10:99167048..99167690-chr10:99202933..99203496,3	MCF-7	breast:
4	chr10:99166608..99167808-chr10:99223063..99223942,3	K562	blood:
5	chr10:99165638..99168564-chr10:99206419..99208887,2	K562	blood:
6	chr10:99167329..99170303-chr10:99178953..99180930,2	K562	blood:
7	chr10:99159230..99162370-chr10:99166178..99169290,4	K562	blood:
8	chr10:99166902..99167876-chr10:99185470..99186302,2	MCF-7	breast:
9	chr10:99092178..99094562-chr10:99167092..99169004,2	MCF-7	breast:
10	chr10:99167036..99170302-chr10:99173339..99176571,3	MCF-7	breast:
11	chr10:99163654..99167601-chr10:99201565..99206372,5	MCF-7	breast:
12	chr10:99166045..99168504-chr10:99170322..99173005,2	K562	blood:
13	chr10:99166868..99167797-chr10:99193919..99194862,2	K562	blood:
14	chr10:99166916..99167827-chr10:99185028..99186031,4	K562	blood:
15	chr10:99166882..99167838-chr10:99223370..99224268,2	MCF-7	breast:
16	chr10:99167024..99167842-chr10:99193469..99194416,4	MCF-7	breast:
17	chr10:99165495..99167483-chr10:99187813..99189704,2	K562	blood:
18	chr10:99167020..99167837-chr10:99221428..99222089,2	K562	blood:
19	chr10:99164883..99168740-chr10:99185841..99188732,4	K562	blood:
20	chr10:99166657..99167578-chr10:99223483..99224439,2	MCF-7	breast:
21	chr10:99166892..99169975-chr10:99170359..99172836,3	MCF-7	breast:
22	chr10:99167117..99169184-chr10:99173224..99175033,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224474	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000225850	Chromatin interaction
ENSG00000171314	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000231970	Chromatin interaction
ENSG00000171311	Chromatin interaction
ENSG00000181274	Chromatin interaction
ENSG00000200737	Chromatin interaction
ENSG00000052749	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10882905	0.91[CHB][hapmap]
rs10882927	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1334891	0.86[CHB][hapmap]
rs2275580	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs4919096	0.86[CHB][hapmap]
rs7090847	0.81[AMR][1000 genomes]
rs7898743	0.85[EUR][1000 genomes]
rs7919862	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7923907	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs954148	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467437	chr10:99115683-99167436	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv552023	chr10:99115683-99167436	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv467438	chr10:99126249-99173870	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv552024	chr10:99126249-99173870	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv467440	chr10:99134784-99204791	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv552025	chr10:99134784-99204791	Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7895646	FRAT1	cis	multi-tissue	Pritchard
rs7895646	RRP12	cis	cerebellum	SCAN
rs7895646	KIAA0690	cis	multi-tissue	Pritchard
rs7895646	RRP12	cis	parietal	SCAN
rs7895646	RRP12	cis	Muscle Skeletal	GTEx
rs7895646	RRP12	cis	Heart Left Ventricle	GTEx
rs7895646	FRAT2	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99161600-99178800	Weak transcription	Fetal Stomach	stomach
2	chr10:99161600-99185200	Weak transcription	Pancreas	Pancrea
3	chr10:99164200-99170200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:99164800-99167600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:99165000-99169400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr10:99165400-99168000	Enhancers	Primary hematopoietic stem cells	blood
7	chr10:99165400-99168800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr10:99165800-99169000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:99166000-99167600	Enhancers	Primary B cells from peripheral blood	blood
10	chr10:99166000-99168600	Enhancers	NHEK	skin
11	chr10:99166000-99168800	Enhancers	HMEC	breast
12	chr10:99166200-99167600	Enhancers	Adipose Nuclei	Adipose
13	chr10:99166400-99167600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr10:99166400-99169000	Enhancers	Placenta	Placenta
15	chr10:99166600-99169000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr10:99166800-99167600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr10:99166800-99167600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr10:99166800-99167600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr10:99166800-99167600	Enhancers	Colonic Mucosa	Colon
20	chr10:99166800-99167600	Enhancers	Fetal Intestine Small	intestine
21	chr10:99166800-99168800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr10:99167000-99167600	Active TSS	H9 Cell Line	embryonic stem cell
23	chr10:99167000-99167600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr10:99167000-99167600	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr10:99167000-99167600	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr10:99167000-99167600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr10:99167000-99167600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:99167000-99167600	Enhancers	Fetal Muscle Leg	muscle
29	chr10:99167000-99167600	Enhancers	Dnd41	blood
30	chr10:99167000-99167600	Flanking Active TSS	K562	blood
31	chr10:99167000-99167800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr10:99167000-99167800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr10:99167000-99168000	Enhancers	Placenta Amnion	Placenta Amnion
34	chr10:99167000-99168800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:99167000-99169000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr10:99167200-99167600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr10:99167200-99167600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:99167200-99167600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr10:99167200-99167600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr10:99167200-99167600	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr10:99167200-99167600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr10:99167200-99167600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr10:99167200-99167600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr10:99167200-99167600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr10:99167200-99167600	Enhancers	Brain Angular Gyrus	brain
46	chr10:99167200-99167600	Enhancers	Brain Cingulate Gyrus	brain
47	chr10:99167200-99167600	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr10:99167200-99167600	Enhancers	Esophagus	oesophagus
49	chr10:99167200-99167600	Enhancers	Fetal Brain Male	brain
50	chr10:99167200-99167600	Flanking Active TSS	Fetal Heart	heart

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