Variant report

Variant	rs1168671
Chromosome Location	chr12:122229848-122229849
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122228992..122246947-chr12:122322343..122339116,70	MCF-7	breast:
2	chr12:122229616..122230309-chr7:23145320..23146072,2	Hela-S3	cervix:
3	chr12:122229734..122230507-chr2:69664172..69665149,2	Hela-S3	cervix:
4	chr12:122149249..122152147-chr12:122229581..122233327,7	MCF-7	breast:
5	chr12:122228836..122242951-chr12:122324438..122335797,34	K562	blood:
6	chr12:122188669..122193873-chr12:122227176..122233304,8	MCF-7	breast:
7	chr12:122228999..122246158-chr12:122324401..122342013,93	MCF-7	breast:
8	chr12:120727170..120730056-chr12:122229573..122231675,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000122550	Chromatin interaction
ENSG00000169599	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000230658	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000256950	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1004390	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11043202	0.92[EUR][1000 genomes]
rs11043203	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11043207	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1168663	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1168664	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168665	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1168666	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1168668	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168669	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168672	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1168673	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837955	0.81[ASN][1000 genomes]
rs12303659	0.81[ASN][1000 genomes]
rs12307227	0.91[EUR][1000 genomes]
rs12823194	0.80[EUR][1000 genomes]
rs12832268	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs12832320	0.86[ASN][1000 genomes]
rs1667578	0.92[EUR][1000 genomes]
rs1667579	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1795965	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1795966	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2019561	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2019562	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2122266	0.91[EUR][1000 genomes]
rs2707066	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2707067	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28493021	0.86[ASN][1000 genomes]
rs34226605	0.86[ASN][1000 genomes]
rs712852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136373	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7300684	0.86[ASN][1000 genomes]
rs7308123	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7308348	0.86[ASN][1000 genomes]
rs73413732	0.83[ASN][1000 genomes]
rs7957564	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7974348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895951	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs895952	0.92[EUR][1000 genomes]
rs895953	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs895954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895957	1.00[CEU][hapmap];0.80[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs921286	1.00[CEU][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs921287	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs930665	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1168671	MPHOSPH9	cis	cerebellum	SCAN
rs1168671	SBNO1	cis	parietal	SCAN
rs1168671	LOC338799	cis	parietal	SCAN
rs1168671	LOC338799	cis	cerebellum	SCAN
rs1168671	CCDC60	cis	parietal	SCAN
rs1168671	AC084018.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122206400-122230600	Weak transcription	Brain Angular Gyrus	brain
2	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
4	chr12:122217800-122230400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:122219200-122230600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:122219200-122230600	Weak transcription	Fetal Brain Female	brain
7	chr12:122219600-122230800	Weak transcription	Brain Germinal Matrix	brain
8	chr12:122220400-122230400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr12:122220400-122230600	Weak transcription	Brain Anterior Caudate	brain
10	chr12:122220600-122230400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:122220600-122230400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr12:122221200-122230600	Weak transcription	Right Atrium	heart
13	chr12:122223200-122231400	Weak transcription	HSMM	muscle
14	chr12:122224600-122231200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:122224800-122231000	Weak transcription	Osteobl	bone
16	chr12:122225200-122231400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:122225400-122230000	Enhancers	Spleen	Spleen
18	chr12:122225400-122231000	Weak transcription	Pancreas	Pancrea
19	chr12:122225600-122230400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr12:122225800-122233200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr12:122227200-122231600	Weak transcription	K562	blood
22	chr12:122227400-122232000	Active TSS	Rectal Smooth Muscle	rectum
23	chr12:122227600-122230400	Weak transcription	Small Intestine	intestine
24	chr12:122227800-122230200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:122227800-122230400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:122228200-122230600	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:122228200-122230800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
28	chr12:122228400-122230000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:122228400-122230000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:122228400-122230000	Weak transcription	Fetal Stomach	stomach
31	chr12:122228400-122230200	Weak transcription	Liver	Liver
32	chr12:122228400-122230800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr12:122228400-122231000	Weak transcription	NH-A	brain
34	chr12:122228400-122231200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:122228600-122230000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:122228600-122230000	Weak transcription	Left Ventricle	heart
37	chr12:122228600-122230000	Enhancers	Dnd41	blood
38	chr12:122228600-122230200	Weak transcription	Lung	lung
39	chr12:122228600-122230400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:122228600-122230600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:122228600-122230600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr12:122228600-122230600	Weak transcription	Right Ventricle	heart
43	chr12:122228600-122230800	Weak transcription	Adipose Nuclei	Adipose
44	chr12:122228600-122232400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:122228800-122230000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr12:122228800-122230200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:122228800-122230200	Active TSS	Colonic Mucosa	Colon
48	chr12:122228800-122230600	Weak transcription	Gastric	stomach
49	chr12:122229200-122230000	Transcr. at gene 5' and 3'	A549	lung
50	chr12:122229200-122230200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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