Variant report

Variant	rs12672142
Chromosome Location	chr7:39988551-39988552
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	ELF1	chr7:39988502-39990278	K562	blood:	n/a	chr7:39989855-39989864 chr7:39989461-39989473 chr7:39989457-39989466 chr7:39989460-39989469 chr7:39989854-39989865 chr7:39989466-39989475 chr7:39989854-39989865 chr7:39990120-39990132 chr7:39989463-39989472 chr7:39990213-39990225 chr7:39989458-39989470
2	TAF1	chr7:39988499-39990252	A549	lung:	n/a	n/a
3	POLR2A	chr7:39987966-39990607	HepG2	liver:	n/a	n/a
4	WRNIP1	chr7:39988550-39989348	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:39988029-39991666	GM18951	blood:	n/a	n/a
6	MAX	chr7:39988507-39990207	MCF-7	breast:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
7	GABPA	chr7:39988551-39990399	K562	blood:	n/a	n/a
8	RUNX3	chr7:39988015-39989512	GM12878	blood:	n/a	n/a
9	POLR2A	chr7:39987755-39991690	Hela-S3	cervix:	n/a	n/a
10	ELF1	chr7:39988503-39990372	SK-N-SH	brain:	n/a	chr7:39989855-39989864 chr7:39989461-39989473 chr7:39989457-39989466 chr7:39989460-39989469 chr7:39989854-39989865 chr7:39989466-39989475 chr7:39989854-39989865 chr7:39990120-39990132 chr7:39989463-39989472 chr7:39990213-39990225 chr7:39989458-39989470
11	TAF1	chr7:39988537-39990086	GM12878	blood:	n/a	n/a
12	POLR2A	chr7:39988536-39990398	GM12891	blood:	n/a	n/a
13	POLR2A	chr7:39988207-39990486	HL-60	blood:	n/a	n/a
14	POLR2A	chr7:39988525-39990425	PANC-1	pancreas:	n/a	n/a
15	JUN	chr7:39987759-39990550	K562	blood:	n/a	n/a
16	RCOR1	chr7:39987895-39990293	IMR90	lung:	n/a	n/a
17	ZNF384	chr7:39988205-39990020	K562	blood:	n/a	n/a
18	REST	chr7:39988516-39990440	HL-60	blood:	n/a	chr7:39989330-39989343 chr7:39989948-39989958 chr7:39990212-39990225
19	EP300	chr7:39988351-39990039	GM12878	blood:	n/a	chr7:39989388-39989404 chr7:39989784-39989797 chr7:39989476-39989490 chr7:39989462-39989471 chr7:39989452-39989468 chr7:39989459-39989468 chr7:39989454-39989470 chr7:39989465-39989474 chr7:39989108-39989115
20	STAT5A	chr7:39988148-39990384	GM12878	blood:	n/a	chr7:39989788-39989800 chr7:39989360-39989372 chr7:39989897-39989909
21	E2F6	chr7:39988513-39990126	A549	lung:	n/a	chr7:39989418-39989427 chr7:39989464-39989474 chr7:39989896-39989905 chr7:39989458-39989468 chr7:39989461-39989471
22	SMC3	chr7:39987729-39992298	SK-N-SH	brain:	n/a	chr7:39989125-39989135
23	RUNX3	chr7:39988137-39990520	GM12878	blood:	n/a	n/a
24	FOXM1	chr7:39988329-39990489	GM12878	blood:	n/a	n/a
25	SP1	chr7:39988510-39989523	GM12878	blood:	n/a	chr7:39989360-39989374 chr7:39989333-39989347 chr7:39989354-39989368 chr7:39989416-39989430 chr7:39989168-39989179 chr7:39989281-39989295
26	MAX	chr7:39988411-39990565	GM12878	blood:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
27	POLR2A	chr7:39988042-39992281	IMR90	lung:	n/a	n/a
28	MYC	chr7:39988532-39990250	K562	blood:	n/a	chr7:39989183-39989193 chr7:39989411-39989421
29	POLR2A	chr7:39988519-39991740	GM12878	blood:	n/a	n/a
30	BHLHE40	chr7:39987846-39988555	GM12878	blood:	n/a	n/a
31	GABPA	chr7:39988527-39990363	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr7:39987471-39990419	GM12891	blood:	n/a	n/a
33	MTA3	chr7:39988545-39989186	GM12878	blood:	n/a	n/a
34	ATF2	chr7:39988181-39990121	GM12878	blood:	n/a	n/a
35	PAX5	chr7:39988440-39990418	GM12878	blood:	n/a	chr7:39989226-39989235 chr7:39989107-39989116
36	POLR2A	chr7:39988536-39991648	MCF-7	breast:	n/a	n/a
37	POLR2A	chr7:39987996-39990509	MCF10A-Er-Src	breast:	n/a	n/a
38	PML	chr7:39988005-39990723	GM12878	blood:	n/a	chr7:39989206-39989214
39	MTA3	chr7:39987685-39990463	GM12878	blood:	n/a	n/a
40	TAF1	chr7:39988546-39989274	GM12878	blood:	n/a	n/a
41	CHD1	chr7:39988142-39993006	IMR90	lung:	n/a	chr7:39989417-39989427
42	YY1	chr7:39988479-39990109	GM12878	blood:	n/a	chr7:39989466-39989475 chr7:39989458-39989469 chr7:39989524-39989535 chr7:39989457-39989471 chr7:39989418-39989429 chr7:39989464-39989475 chr7:39989463-39989472 chr7:39989877-39989891 chr7:39989461-39989472 chr7:39989457-39989466 chr7:39989377-39989391 chr7:39989460-39989474 chr7:39989454-39989468 chr7:39989460-39989469
43	PRDM1	chr7:39988219-39988559	Hela-S3	cervix:	n/a	chr7:39988379-39988393
44	RELA	chr7:39988250-39990184	GM15510	blood:	n/a	n/a
45	GABPA	chr7:39988537-39990307	A549	lung:	n/a	n/a
46	RELA	chr7:39988118-39990205	GM12891	blood:	n/a	n/a
47	POLR2A	chr7:39988504-39991610	K562	blood:	n/a	n/a
48	POLR2A	chr7:39987933-39990185	GM12892	blood:	n/a	n/a
49	IRF4	chr7:39988518-39989243	GM12878	blood:	n/a	n/a
50	CEBPB	chr7:39988197-39989401	A549	lung:	n/a	chr7:39988351-39988362

No.	Distal block	Cell Line	Cell type
1	chr1:94311521..94312144-chr7:39988387..39989256,2	HCT-116	colon:
2	chr7:39987485..39989678-chr7:40173138..40176244,4	K562	blood:
3	chr7:39663090..39665724-chr7:39988469..39990285,2	MCF-7	breast:
4	chr7:39987353..39988943-chr7:40114287..40116137,2	K562	blood:
5	chr7:39605012..39607338-chr7:39986740..39989686,2	K562	blood:
6	chr7:39988519..39989328-chr8:144911030..144911895,2	HCT-116	colon:
7	chr7:39987649..39989294-chr7:40160123..40163099,2	K562	blood:
8	chr7:39987318..39990027-chr8:101962750..101965742,2	MCF-7	breast:
9	chr11:107879571..107880146-chr7:39988538..39989329,2	Hela-S3	cervix:
10	chr7:39963368..39965638-chr7:39986641..39989237,2	K562	blood:
11	chr7:39986663..39989008-chr7:40035472..40037902,2	K562	blood:
12	chr7:39987721..39990242-chr7:40174056..40176267,2	MCF-7	breast:
13	chr6:74230266..74231191-chr7:39988525..39989555,3	Hela-S3	cervix:
14	chr7:39985235..39991458-chr7:40172332..40176244,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf11-1	chr7:39987121-39989354	ENSG00000259826.1

Variant related genes	Relation type
CDK13	TF binding region
ENSG00000166266	Chromatin interaction
ENSG00000175600	Chromatin interaction
ENSG00000168303	Chromatin interaction
ENSG00000164924	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000227172	Chromatin interaction
ENSG00000179950	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10233552	0.97[EUR][1000 genomes]
rs10252631	0.97[EUR][1000 genomes]
rs10261984	0.82[EUR][1000 genomes]
rs1082028	0.95[ASN][1000 genomes]
rs1082030	0.86[ASN][1000 genomes]
rs10951623	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10951624	0.97[EUR][1000 genomes]
rs10951625	1.00[EUR][1000 genomes]
rs11972983	1.00[EUR][1000 genomes]
rs11977756	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11983287	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12530835	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531761	1.00[EUR][1000 genomes]
rs12531774	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12532714	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534103	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12535281	0.87[EUR][1000 genomes]
rs12536190	1.00[EUR][1000 genomes]
rs12536349	0.92[EUR][1000 genomes]
rs12536726	1.00[EUR][1000 genomes]
rs12537125	1.00[EUR][1000 genomes]
rs12537320	1.00[EUR][1000 genomes]
rs12539956	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1257698	0.97[EUR][1000 genomes]
rs1257699	0.91[ASN][1000 genomes]
rs12666454	0.98[EUR][1000 genomes]
rs12669872	1.00[EUR][1000 genomes]
rs12672040	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12672136	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13438258	0.87[EUR][1000 genomes]
rs13438262	0.87[EUR][1000 genomes]
rs13438324	0.87[EUR][1000 genomes]
rs17171637	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17171645	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17171646	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17496429	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17496670	0.97[EUR][1000 genomes]
rs17496733	1.00[EUR][1000 genomes]
rs17537767	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17538125	1.00[EUR][1000 genomes]
rs2015842	1.00[EUR][1000 genomes]
rs2159489	0.93[EUR][1000 genomes]
rs2302341	1.00[EUR][1000 genomes]
rs2329615	0.87[EUR][1000 genomes]
rs28627647	0.84[EUR][1000 genomes]
rs28879668	0.87[EUR][1000 genomes]
rs3735135	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800799	0.98[EUR][1000 genomes]
rs3801238	0.98[EUR][1000 genomes]
rs3847019	1.00[EUR][1000 genomes]
rs3911836	1.00[EUR][1000 genomes]
rs3911889	1.00[EUR][1000 genomes]
rs4344004	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4720344	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4720347	0.97[EUR][1000 genomes]
rs4720349	0.97[EUR][1000 genomes]
rs4723923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723925	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4723927	1.00[EUR][1000 genomes]
rs4723928	1.00[EUR][1000 genomes]
rs60315659	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6961040	0.87[EUR][1000 genomes]
rs6963973	0.87[EUR][1000 genomes]
rs6967332	0.87[EUR][1000 genomes]
rs6970469	0.84[EUR][1000 genomes]
rs758696	1.00[EUR][1000 genomes]
rs773379	0.83[ASN][1000 genomes]
rs773381	0.84[ASN][1000 genomes]
rs773385	0.91[ASN][1000 genomes]
rs773386	0.92[ASN][1000 genomes]
rs773393	0.80[ASN][1000 genomes]
rs773397	0.80[ASN][1000 genomes]
rs773403	0.93[ASN][1000 genomes]
rs773411	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs773414	0.95[ASN][1000 genomes]
rs773415	0.86[ASN][1000 genomes]
rs773424	0.92[ASN][1000 genomes]
rs7779663	1.00[EUR][1000 genomes]
rs7799846	0.83[ASN][1000 genomes]
rs940272	0.89[AMR][1000 genomes];0.89[EUR][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	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39987600-39988600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr7:39987600-39989000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr7:39987800-39988600	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr7:39987800-39988600	Flanking Active TSS	Primary T cells from cord blood	blood
5	chr7:39987800-39988600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr7:39987800-39988800	Active TSS	Right Atrium	heart
7	chr7:39987800-39992800	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr7:39987800-39993200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr7:39987800-39993400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr7:39988000-39988600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
11	chr7:39988000-39988600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:39988000-39988600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
13	chr7:39988000-39988600	Flanking Active TSS	Liver	Liver
14	chr7:39988000-39988600	Enhancers	Small Intestine	intestine
15	chr7:39988000-39988600	Flanking Active TSS	Hela-S3	cervix
16	chr7:39988000-39989000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr7:39988000-39989000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
18	chr7:39988000-39989600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:39988000-39990600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:39988000-39991400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:39988000-39991400	Active TSS	Esophagus	oesophagus
22	chr7:39988000-39991800	Active TSS	Gastric	stomach
23	chr7:39988000-39991800	Active TSS	Left Ventricle	heart
24	chr7:39988000-39991800	Active TSS	Pancreas	Pancrea
25	chr7:39988000-39992000	Active TSS	Stomach Mucosa	stomach
26	chr7:39988000-39992200	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr7:39988000-39992400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr7:39988000-39992800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:39988000-39993000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr7:39988000-39993200	Active TSS	HSMM	muscle
31	chr7:39988000-39993400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:39988000-39993400	Active TSS	Osteobl	bone
33	chr7:39988000-39993600	Active TSS	Colonic Mucosa	Colon
34	chr7:39988000-39993800	Active TSS	ES-I3 Cell Line	embryonic stem cell
35	chr7:39988000-39993800	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr7:39988000-39994000	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr7:39988200-39988800	Weak transcription	Spleen	Spleen
38	chr7:39988200-39989600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr7:39988200-39991000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:39988200-39991800	Active TSS	Lung	lung
41	chr7:39988200-39992200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr7:39988200-39992800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:39988200-39993200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr7:39988200-39993200	Active TSS	H9 Cell Line	embryonic stem cell
45	chr7:39988200-39993200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:39988200-39993200	Active TSS	Muscle Satellite Cultured Cells	--
47	chr7:39988200-39993200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:39988200-39993200	Active TSS	Colon Smooth Muscle	Colon
49	chr7:39988200-39993200	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr7:39988200-39993200	Active TSS	A549	lung

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