Variant report

Variant	rs12095412
Chromosome Location	chr1:45299644-45299645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45294943..45299898-chr1:45475782..45481648,8	K562	blood:
2	chr1:45299058..45301658-chr1:45477513..45480027,2	K562	blood:
3	chr1:45298868..45300708-chr1:45804153..45806049,2	K562	blood:
4	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
5	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
6	chr1:45298794..45301202-chr1:45313186..45315040,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142959	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000234093	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000200169	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:150)

rs_ID	r²[population]
rs10157761	0.84[EUR][1000 genomes]
rs10159318	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs10218751	0.83[EUR][1000 genomes]
rs1022814	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs1114390	0.87[EUR][1000 genomes]
rs11211042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211043	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211052	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs11211061	0.80[EUR][1000 genomes]
rs11211062	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs11211063	0.94[CEU][hapmap]
rs114833	0.88[EUR][1000 genomes]
rs11573589	0.87[YRI][hapmap]
rs12057238	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12080887	0.90[EUR][1000 genomes]
rs12093313	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12402452	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs12402781	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs12403201	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs12404127	0.86[EUR][1000 genomes]
rs12404168	0.89[EUR][1000 genomes]
rs12404244	0.85[ASN][1000 genomes]
rs12405110	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12405721	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs12407290	1.00[CEU][hapmap]
rs12407565	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs12408763	0.92[EUR][1000 genomes]
rs12410088	0.88[EUR][1000 genomes]
rs12411070	0.87[EUR][1000 genomes]
rs13374816	0.89[EUR][1000 genomes]
rs1392035	0.85[EUR][1000 genomes]
rs1572379	0.88[EUR][1000 genomes]
rs1627320	0.87[EUR][1000 genomes]
rs16832249	0.93[CHB][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16832251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16832301	0.94[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs17390300	0.91[EUR][1000 genomes]
rs17390328	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17390356	0.91[EUR][1000 genomes]
rs17390398	0.91[EUR][1000 genomes]
rs17390824	0.89[EUR][1000 genomes]
rs17390859	0.84[EUR][1000 genomes]
rs17390900	0.84[EUR][1000 genomes]
rs17390983	0.84[EUR][1000 genomes]
rs17392632	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs174636	0.86[EUR][1000 genomes]
rs2078329	0.83[EUR][1000 genomes]
rs2102035	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2133501	0.89[EUR][1000 genomes]
rs2261859	0.81[EUR][1000 genomes]
rs2295996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs263960	0.89[EUR][1000 genomes]
rs263961	0.88[EUR][1000 genomes]
rs263967	0.87[EUR][1000 genomes]
rs263971	0.88[EUR][1000 genomes]
rs263979	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs263981	0.87[EUR][1000 genomes]
rs264002	0.94[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs264004	0.81[EUR][1000 genomes]
rs264006	0.81[EUR][1000 genomes]
rs264007	0.81[EUR][1000 genomes]
rs28700974	0.83[EUR][1000 genomes]
rs28707013	0.83[EUR][1000 genomes]
rs28819230	0.81[EUR][1000 genomes]
rs35700678	0.88[EUR][1000 genomes]
rs371098	0.81[EUR][1000 genomes]
rs3738248	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs3767490	0.90[EUR][1000 genomes]
rs3795718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3889352	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs3889822	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs3923304	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs392410	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs4073112	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs4082644	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs41269085	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs427392	0.81[EUR][1000 genomes]
rs435311	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4415616	0.87[EUR][1000 genomes]
rs441876	0.81[EUR][1000 genomes]
rs4424549	0.89[EUR][1000 genomes]
rs4472791	0.87[EUR][1000 genomes]
rs4515833	0.87[EUR][1000 genomes]
rs471564	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs539409	0.81[EUR][1000 genomes]
rs546354	0.81[EUR][1000 genomes]
rs55708712	0.91[EUR][1000 genomes]
rs55756712	0.84[EUR][1000 genomes]
rs55792507	0.89[EUR][1000 genomes]
rs55807836	0.86[EUR][1000 genomes]
rs55851444	0.84[EUR][1000 genomes]
rs55893665	0.91[EUR][1000 genomes]
rs55916129	0.87[EUR][1000 genomes]
rs55926235	0.87[EUR][1000 genomes]
rs56102504	0.87[EUR][1000 genomes]
rs57104118	0.89[EUR][1000 genomes]
rs57769237	0.89[EUR][1000 genomes]
rs58191426	0.90[EUR][1000 genomes]
rs59050077	0.90[EUR][1000 genomes]
rs59552012	0.89[EUR][1000 genomes]
rs59559455	0.88[EUR][1000 genomes]
rs59803789	0.83[ASN][1000 genomes]
rs59938994	0.87[EUR][1000 genomes]
rs60082006	0.84[EUR][1000 genomes]
rs606873	0.81[EUR][1000 genomes]
rs60741033	0.87[EUR][1000 genomes]
rs60787198	0.89[EUR][1000 genomes]
rs608649	0.94[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs61149327	0.93[EUR][1000 genomes]
rs61673889	0.83[EUR][1000 genomes]
rs637224	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs640743	0.81[EUR][1000 genomes]
rs6657078	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6678737	0.82[ASN][1000 genomes]
rs6684417	0.87[EUR][1000 genomes]
rs67058449	0.87[EUR][1000 genomes]
rs72674049	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72674051	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72674064	0.93[EUR][1000 genomes]
rs72674081	0.89[EUR][1000 genomes]
rs72674084	0.90[EUR][1000 genomes]
rs72676504	0.90[EUR][1000 genomes]
rs72676505	0.86[EUR][1000 genomes]
rs72676509	0.90[EUR][1000 genomes]
rs72676513	0.88[EUR][1000 genomes]
rs72676525	0.87[EUR][1000 genomes]
rs72676529	0.87[EUR][1000 genomes]
rs72676536	0.86[EUR][1000 genomes]
rs72676539	0.87[EUR][1000 genomes]
rs72676542	0.87[EUR][1000 genomes]
rs72676550	0.87[EUR][1000 genomes]
rs72676553	0.84[EUR][1000 genomes]
rs72676555	0.87[EUR][1000 genomes]
rs72676557	0.88[EUR][1000 genomes]
rs72676559	0.89[EUR][1000 genomes]
rs72676561	0.87[EUR][1000 genomes]
rs72676563	0.85[EUR][1000 genomes]
rs72676581	0.84[EUR][1000 genomes]
rs72676600	0.80[EUR][1000 genomes]
rs72677810	0.84[EUR][1000 genomes]
rs7515226	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs7519592	0.94[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7529213	0.94[CEU][hapmap];0.93[GIH][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs7529221	0.81[EUR][1000 genomes]
rs7531391	0.87[EUR][1000 genomes]
rs7532882	0.87[YRI][hapmap]
rs7533716	0.85[EUR][1000 genomes]
rs7546853	0.91[EUR][1000 genomes]
rs9662872	0.81[EUR][1000 genomes]
rs9662878	0.81[EUR][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	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
3	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
4	nsv1014894	chr1:45139123-45397943	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	414 gene(s)	inside rSNPs	diseases
5	nsv529677	chr1:45179509-45748571	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	424 gene(s)	inside rSNPs	diseases
6	nsv1002026	chr1:45187594-45758048	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	386 gene(s)	inside rSNPs	diseases
7	nsv870815	chr1:45233638-45318752	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546146	chr1:45258141-45318752	Genic enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	109 gene(s)	inside rSNPs	diseases
9	nsv915644	chr1:45282802-45696079	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12095412	EBNA1BP2	cis	cerebellum	SCAN
rs12095412	STIL	cis	parietal	SCAN
rs12095412	CDC20	cis	cerebellum	SCAN
rs12095412	SNORD55	cis	cerebellum	SCAN
rs12095412	C1orf84	cis	parietal	SCAN
rs12095412	ZNF691	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45286200-45301800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:45286400-45308400	Weak transcription	Aorta	Aorta
3	chr1:45286600-45301600	Weak transcription	Right Atrium	heart
4	chr1:45286600-45301800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:45286800-45301600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr1:45287000-45301800	Weak transcription	Thymus	Thymus
7	chr1:45287200-45307400	Weak transcription	Colon Smooth Muscle	Colon
8	chr1:45289400-45307600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:45292200-45301800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:45292400-45308200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:45292800-45301400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:45293000-45301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:45293000-45301800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:45293400-45301400	Weak transcription	Pancreas	Pancrea
15	chr1:45293800-45301400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:45294000-45308200	Weak transcription	Gastric	stomach
17	chr1:45294400-45301600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:45295000-45300800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr1:45295400-45302000	Weak transcription	Fetal Brain Female	brain
20	chr1:45295400-45308400	Weak transcription	Right Ventricle	heart
21	chr1:45295800-45300800	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr1:45295800-45301400	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:45295800-45301400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:45295800-45305600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:45295800-45308000	Weak transcription	Brain Germinal Matrix	brain
26	chr1:45296000-45300800	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:45296000-45301400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:45296000-45301800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:45296000-45307600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr1:45296600-45301400	Weak transcription	Brain Substantia Nigra	brain
31	chr1:45296800-45300000	Weak transcription	Lung	lung
32	chr1:45297000-45305200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:45297000-45305200	Weak transcription	Ovary	ovary
34	chr1:45297200-45301600	Weak transcription	Primary T cells from cord blood	blood
35	chr1:45297400-45301400	Weak transcription	Stomach Mucosa	stomach
36	chr1:45297400-45305200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:45297600-45303200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:45297800-45301400	Weak transcription	GM12878-XiMat	blood
39	chr1:45298000-45301400	Weak transcription	Fetal Kidney	kidney
40	chr1:45298000-45305200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:45298000-45305400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:45298000-45308200	Weak transcription	Spleen	Spleen
43	chr1:45298200-45300000	Weak transcription	Placenta	Placenta
44	chr1:45298200-45301400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr1:45298200-45301400	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:45298200-45301800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:45298200-45305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:45298400-45301600	Strong transcription	Fetal Stomach	stomach
49	chr1:45298400-45301800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr1:45298600-45300800	Enhancers	Primary neutrophils fromperipheralblood	blood

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