Variant report

Variant	rs12407290
Chromosome Location	chr1:45275339-45275340
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr1:45274854-45275687	GM12878	blood:	n/a	n/a
2	MAX	chr1:45272578-45275645	HepG2	liver:	n/a	chr1:45273101-45273110 chr1:45274140-45274149 chr1:45272888-45272897 chr1:45272902-45272912 chr1:45273819-45273828 chr1:45273217-45273226 chr1:45272889-45272898 chr1:45273195-45273211 chr1:45274136-45274145
3	POLR2A	chr1:45274858-45275438	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:45275210-45275595	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:45270630-45276680	Hela-S3	cervix:	n/a	n/a
6	POU2F2	chr1:45274953-45275987	GM12891	blood:	n/a	n/a
7	TCF3	chr1:45275229-45275542	GM12878	blood:	n/a	n/a
8	RUNX3	chr1:45274662-45276517	GM12878	blood:	n/a	n/a
9	PAX5	chr1:45275047-45276443	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:45270697-45276683	GM12892	blood:	n/a	n/a
11	RELA	chr1:45274946-45276608	GM19193	blood:	n/a	n/a
12	TAF1	chr1:45275141-45275478	GM12891	blood:	n/a	n/a
13	WRNIP1	chr1:45275215-45275660	GM12878	blood:	n/a	n/a
14	BCLAF1	chr1:45274943-45275733	GM12878	blood:	n/a	chr1:45275338-45275347
15	MAZ	chr1:45272658-45275606	K562	blood:	n/a	chr1:45273101-45273110 chr1:45274140-45274149 chr1:45272888-45272897 chr1:45272902-45272912 chr1:45273819-45273828 chr1:45273217-45273226 chr1:45272889-45272898 chr1:45273195-45273211 chr1:45274136-45274145
16	POLR2A	chr1:45275095-45275591	Raji	blood:	n/a	n/a
17	ELF1	chr1:45274940-45275670	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:45272763-45275529	HepG2	liver:	n/a	n/a
19	SPI1	chr1:45275151-45275523	GM12878	blood:	n/a	n/a
20	ZMIZ1	chr1:45275254-45275538	K562	blood:	n/a	n/a
21	POLR2A	chr1:45272295-45276658	GM12891	blood:	n/a	n/a
22	RELA	chr1:45274785-45276509	GM12891	blood:	n/a	n/a
23	EGR1	chr1:45275131-45275568	K562	blood:	n/a	chr1:45275338-45275347 chr1:45275428-45275442
24	NFIC	chr1:45274237-45276485	GM12878	blood:	n/a	n/a
25	TEAD4	chr1:45274910-45275809	K562	blood:	n/a	n/a
26	RELA	chr1:45274883-45276410	GM18505	blood:	n/a	n/a
27	POLR2A	chr1:45274988-45275726	K562	blood:	n/a	n/a
28	POLR2A	chr1:45272323-45275578	K562	blood:	n/a	n/a
29	RCOR1	chr1:45274800-45276343	GM12878	blood:	n/a	n/a
30	ZNF384	chr1:45275269-45275611	GM12878	blood:	n/a	n/a
31	HEY1	chr1:45272708-45275606	HepG2	liver:	n/a	chr1:45274208-45274223 chr1:45274211-45274226
32	POU2F2	chr1:45274955-45275631	GM12891	blood:	n/a	n/a
33	JUN	chr1:45272369-45276076	K562	blood:	n/a	chr1:45275369-45275380 chr1:45274847-45274856 chr1:45272889-45272897 chr1:45272997-45273005 chr1:45272888-45272898 chr1:45273214-45273225 chr1:45273218-45273226 chr1:45272996-45273007 chr1:45272888-45272897 chr1:45273219-45273226 chr1:45273217-45273227 chr1:45272889-45272896 chr1:45272996-45273006 chr1:45273218-45273226 chr1:45272996-45273006 chr1:45272887-45272899
34	NFIC	chr1:45274845-45275634	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:45275043-45275576	GM15510	blood:	n/a	n/a
36	EGR1	chr1:45275194-45275547	GM12878	blood:	n/a	chr1:45275338-45275347 chr1:45275428-45275442
37	POLR2A	chr1:45270657-45276553	K562	blood:	n/a	n/a
38	STAT5A	chr1:45274839-45275534	GM12878	blood:	n/a	chr1:45274969-45274977
39	POLR2A	chr1:45272201-45276585	GM12891	blood:	n/a	n/a
40	ELK1	chr1:45275003-45275714	GM12878	blood:	n/a	chr1:45275338-45275347 chr1:45275338-45275347
41	EBF1	chr1:45274898-45276561	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:45272161-45276552	GM12892	blood:	n/a	n/a
43	NFIC	chr1:45275190-45276393	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr1:45274876-45275440	K562	blood:	n/a	n/a
45	STAT1	chr1:45275265-45275464	GM12878	blood:	n/a	n/a
46	MAFK	chr1:45275297-45275658	HepG2	liver:	n/a	chr1:45275467-45275482 chr1:45275468-45275479
47	POLR2A	chr1:45275034-45276230	U87	brain:	n/a	n/a
48	YY1	chr1:45275147-45275594	GM12878	blood:	n/a	n/a
49	TBP	chr1:45275128-45275671	GM12878	blood:	n/a	n/a
50	SP1	chr1:45275076-45275628	GM12878	blood:	n/a	chr1:45275429-45275439 chr1:45275513-45275522

No.	Distal block	Cell Line	Cell type
1	chr1:45190324..45200952-chr1:45272085..45288310,59	MCF-7	breast:
2	chr1:45185720..45187658-chr1:45273782..45275923,3	MCF-7	breast:
3	chr1:45184399..45189674-chr1:45270870..45279135,15	MCF-7	breast:
4	chr1:45273964..45275771-chr1:45451640..45453619,2	K562	blood:
5	chr1:45238319..45262026-chr1:45262351..45301953,358	K562	blood:
6	chr1:45194189..45198394-chr1:45270401..45277394,13	MCF-7	breast:
7	chr1:45273605..45276582-chr1:45986789..45988627,2	K562	blood:
8	chr1:45178001..45208867-chr1:45262751..45305400,520	K562	blood:
9	chr1:45272934..45277358-chr1:45964626..45967668,4	K562	blood:
10	chr1:45239942..45244585-chr1:45273690..45277023,5	MCF-7	breast:
11	chr1:45178748..45209946-chr1:45262890..45299284,515	K562	blood:
12	chr1:45273315..45275597-chr1:45475668..45479411,4	K562	blood:

Variant related genes	Relation type
BTBD19	TF binding region
TCTEX1D4	TF binding region
ENSG00000200169	Chromatin interaction
ENSG00000202031	Chromatin interaction
ENSG00000070785	Chromatin interaction
ENSG00000126107	Chromatin interaction
ENSG00000225721	Chromatin interaction
ENSG00000142959	Chromatin interaction
ENSG00000236624	Chromatin interaction
ENSG00000207421	Chromatin interaction
ENSG00000200913	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000264294	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000142945	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000142937	Chromatin interaction
ENSG00000126088	Chromatin interaction
ENSG00000234093	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10159318	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1022814	0.94[CEU][hapmap]
rs11211042	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs11211043	0.82[EUR][1000 genomes]
rs11211052	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs11211062	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs11211063	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12057238	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs12057414	0.91[ASN][1000 genomes]
rs12093313	0.94[CEU][hapmap]
rs12095412	1.00[CEU][hapmap]
rs12402452	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs12402781	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs12403201	0.89[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs12404160	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12404244	0.91[EUR][1000 genomes]
rs12405110	0.83[EUR][1000 genomes]
rs12405721	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs12407565	0.94[CEU][hapmap]
rs12407627	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12408763	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16832249	0.80[EUR][1000 genomes]
rs16832251	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs16832301	0.94[CEU][hapmap]
rs17390328	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17390356	0.82[ASN][1000 genomes]
rs17390398	0.84[ASN][1000 genomes]
rs17391430	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs17392632	0.94[CEU][hapmap]
rs17883304	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17885815	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2102035	0.87[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2265603	1.00[YRI][hapmap]
rs2295996	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs263979	0.88[CEU][hapmap]
rs263984	1.00[YRI][hapmap]
rs264001	1.00[YRI][hapmap]
rs264002	0.94[CEU][hapmap]
rs264012	1.00[YRI][hapmap]
rs264017	1.00[YRI][hapmap]
rs3738248	0.88[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs3795712	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3795715	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3795718	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs3806398	0.90[ASN][1000 genomes]
rs3889352	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3889822	0.89[CEU][hapmap]
rs3923304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392410	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4073112	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs4082644	0.94[CEU][hapmap]
rs411976	1.00[YRI][hapmap]
rs41269079	0.90[ASN][1000 genomes]
rs41269085	0.84[EUR][1000 genomes]
rs435311	0.89[CEU][hapmap]
rs4520451	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4565758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471564	0.89[CEU][hapmap]
rs474207	1.00[YRI][hapmap]
rs492515	1.00[YRI][hapmap]
rs506691	1.00[YRI][hapmap]
rs55703843	0.85[ASN][1000 genomes]
rs55708712	0.84[ASN][1000 genomes]
rs55893665	0.84[ASN][1000 genomes]
rs58191426	0.84[ASN][1000 genomes]
rs58603818	0.82[ASN][1000 genomes]
rs59803789	0.91[EUR][1000 genomes]
rs59895800	0.88[ASN][1000 genomes]
rs60189524	0.88[EUR][1000 genomes]
rs60452778	0.83[ASN][1000 genomes]
rs608649	0.94[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs61149327	0.84[ASN][1000 genomes]
rs637224	0.88[CEU][hapmap]
rs6657078	0.81[EUR][1000 genomes]
rs6678737	0.90[EUR][1000 genomes]
rs72674017	0.88[ASN][1000 genomes]
rs72674023	0.90[ASN][1000 genomes]
rs72674049	0.80[EUR][1000 genomes]
rs72674051	0.83[EUR][1000 genomes]
rs72674064	0.84[ASN][1000 genomes]
rs7515226	0.94[CEU][hapmap]
rs7519592	0.94[CEU][hapmap]
rs7529213	0.94[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv461406	chr1:45218542-45293518	Strong transcription Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
8	nsv546145	chr1:45218542-45293518	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	127 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv870773	chr1:45259295-45287306	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	108 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45265600-45276600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:45266600-45276400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:45270000-45278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:45271800-45277400	Weak transcription	Ovary	ovary
5	chr1:45272000-45278000	Enhancers	Primary hematopoietic stem cells	blood
6	chr1:45272200-45275600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:45272400-45275600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr1:45272400-45275800	Flanking Active TSS	Rectal Smooth Muscle	rectum
9	chr1:45272400-45276000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:45272400-45276200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr1:45272400-45276400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:45272400-45276600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:45272400-45276600	Enhancers	Pancreas	Pancrea
14	chr1:45272400-45277600	Enhancers	Primary B cells from peripheral blood	blood
15	chr1:45272600-45275400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr1:45272600-45276400	Enhancers	Aorta	Aorta
17	chr1:45272600-45276400	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr1:45272600-45276800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr1:45272600-45277000	Enhancers	Lung	lung
20	chr1:45272800-45275600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:45272800-45275600	Flanking Active TSS	Osteobl	bone
22	chr1:45272800-45276200	Enhancers	Spleen	Spleen
23	chr1:45272800-45276200	Flanking Active TSS	HSMM	muscle
24	chr1:45272800-45276400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:45272800-45276400	Enhancers	Dnd41	blood
26	chr1:45272800-45276600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:45272800-45277600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr1:45272800-45278000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:45273000-45275400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:45273000-45275800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr1:45273000-45276400	Flanking Active TSS	NH-A	brain
32	chr1:45273000-45278000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:45273200-45275400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr1:45273200-45275600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:45273200-45276000	Flanking Active TSS	NHDF-Ad	bronchial
36	chr1:45273200-45276400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:45273200-45276400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr1:45273400-45275800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:45273400-45276000	Enhancers	Esophagus	oesophagus
40	chr1:45273400-45278000	Enhancers	Brain Substantia Nigra	brain
41	chr1:45273600-45275400	Weak transcription	Psoas Muscle	Psoas
42	chr1:45273600-45276200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:45273600-45276200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:45273600-45276200	Flanking Active TSS	HSMMtube	muscle
45	chr1:45273600-45276400	Enhancers	Small Intestine	intestine
46	chr1:45273600-45276400	Flanking Active TSS	HUVEC	blood vessel
47	chr1:45273600-45277600	Enhancers	Gastric	stomach
48	chr1:45273800-45275400	Flanking Active TSS	Colonic Mucosa	Colon
49	chr1:45273800-45275400	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr1:45273800-45275400	Flanking Active TSS	Fetal Stomach	stomach

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