Variant report

Variant	rs12672136
Chromosome Location	chr7:39988329-39988330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:96)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:96 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:39988033-39988347	K562	blood:	n/a	n/a
2	POLR2A	chr7:39987966-39990607	HepG2	liver:	n/a	n/a
3	POLR2A	chr7:39987980-39988510	HCT-116	colon:	n/a	n/a
4	POLR2A	chr7:39988000-39988461	GM12892	blood:	n/a	n/a
5	POLR2A	chr7:39988029-39991666	GM18951	blood:	n/a	n/a
6	RUNX3	chr7:39988015-39989512	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:39987755-39991690	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr7:39988207-39990486	HL-60	blood:	n/a	n/a
9	JUN	chr7:39987759-39990550	K562	blood:	n/a	n/a
10	RCOR1	chr7:39987895-39990293	IMR90	lung:	n/a	n/a
11	ZNF384	chr7:39988205-39990020	K562	blood:	n/a	n/a
12	EP300	chr7:39988191-39988393	GM12878	blood:	n/a	n/a
13	BHLHE40	chr7:39987958-39988524	K562	blood:	n/a	n/a
14	STAT5A	chr7:39988148-39990384	GM12878	blood:	n/a	chr7:39989788-39989800 chr7:39989360-39989372 chr7:39989897-39989909
15	POLR2A	chr7:39987856-39988502	GM12878	blood:	n/a	n/a
16	SMC3	chr7:39987729-39992298	SK-N-SH	brain:	n/a	chr7:39989125-39989135
17	RUNX3	chr7:39988137-39990520	GM12878	blood:	n/a	n/a
18	FOXM1	chr7:39988329-39990489	GM12878	blood:	n/a	n/a
19	HEY1	chr7:39988174-39988497	HepG2	liver:	n/a	n/a
20	POLR2A	chr7:39988042-39992281	IMR90	lung:	n/a	n/a
21	POLR2A	chr7:39988077-39988489	GM12891	blood:	n/a	n/a
22	BHLHE40	chr7:39987846-39988555	GM12878	blood:	n/a	n/a
23	POLR2A	chr7:39987471-39990419	GM12891	blood:	n/a	n/a
24	ATF2	chr7:39988181-39990121	GM12878	blood:	n/a	n/a
25	POLR2A	chr7:39988284-39988363	MCF-7	breast:	n/a	n/a
26	POLR2A	chr7:39987996-39990509	MCF10A-Er-Src	breast:	n/a	n/a
27	PML	chr7:39988005-39990723	GM12878	blood:	n/a	chr7:39989206-39989214
28	MTA3	chr7:39987685-39990463	GM12878	blood:	n/a	n/a
29	CHD1	chr7:39988142-39993006	IMR90	lung:	n/a	chr7:39989417-39989427
30	PRDM1	chr7:39988219-39988559	Hela-S3	cervix:	n/a	chr7:39988379-39988393
31	RELA	chr7:39988250-39990184	GM15510	blood:	n/a	n/a
32	RELA	chr7:39988118-39990205	GM12891	blood:	n/a	n/a
33	POLR2A	chr7:39987933-39990185	GM12892	blood:	n/a	n/a
34	POLR2A	chr7:39987909-39988476	GM12891	blood:	n/a	n/a
35	POLR2A	chr7:39987990-39988510	GM12891	blood:	n/a	n/a
36	CEBPB	chr7:39988197-39989401	A549	lung:	n/a	chr7:39988351-39988362
37	TBL1XR1	chr7:39988226-39989431	K562	blood:	n/a	n/a
38	NFIC	chr7:39988101-39990082	GM12878	blood:	n/a	n/a
39	SMARCC1	chr7:39988124-39991672	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr7:39987959-39990468	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr7:39987714-39990388	SK-N-SH	brain:	n/a	n/a
42	GABPA	chr7:39988291-39990597	MCF-7	breast:	n/a	n/a
43	POLR2A	chr7:39987988-39990646	K562	blood:	n/a	n/a
44	NR2F2	chr7:39988226-39990181	K562	blood:	n/a	n/a
45	TAL1	chr7:39988218-39989869	K562	blood:	n/a	n/a
46	POLR2A	chr7:39987951-39991615	GM19099	blood:	n/a	n/a
47	CHD1	chr7:39988238-39992105	GM12878	blood:	n/a	chr7:39989417-39989427
48	EP300	chr7:39988325-39988346	GM12878	blood:	n/a	n/a
49	BCLAF1	chr7:39987990-39988386	GM12878	blood:	n/a	n/a
50	HCFC1	chr7:39987813-39992368	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:39987485..39989678-chr7:40173138..40176244,4	K562	blood:
2	chr7:39987353..39988943-chr7:40114287..40116137,2	K562	blood:
3	chr2:64067918..64068649-chr7:39987965..39988470,2	Hela-S3	cervix:
4	chr7:39605012..39607338-chr7:39986740..39989686,2	K562	blood:
5	chr7:39987649..39989294-chr7:40160123..40163099,2	K562	blood:
6	chr7:39987318..39990027-chr8:101962750..101965742,2	MCF-7	breast:
7	chr7:39963368..39965638-chr7:39986641..39989237,2	K562	blood:
8	chr7:39986663..39989008-chr7:40035472..40037902,2	K562	blood:
9	chr7:39987721..39990242-chr7:40174056..40176267,2	MCF-7	breast:
10	chr7:39985235..39991458-chr7:40172332..40176244,8	K562	blood:

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

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

No data

Variant related genes	Relation type
CDK13	TF binding region
ENSG00000164924	Chromatin interaction
ENSG00000168303	Chromatin interaction
ENSG00000241127	Chromatin interaction
ENSG00000227172	Chromatin interaction
ENSG00000169764	Chromatin interaction
ENSG00000175600	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	0.92[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	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11983287	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12530835	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531761	1.00[EUR][1000 genomes]
rs12531774	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12532714	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534103	0.95[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	0.95[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]
rs12672142	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	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17171645	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17171646	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17496429	0.81[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	0.97[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	0.92[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	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4720344	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4720347	0.97[EUR][1000 genomes]
rs4720349	0.97[EUR][1000 genomes]
rs4723923	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4723925	0.92[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	0.92[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	0.92[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	chr7:39987600-39988400	Flanking Active TSS	Dnd41	blood
2	chr7:39987600-39988600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr7:39987600-39989000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:39987800-39988400	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr7:39987800-39988400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr7:39987800-39988400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr7:39987800-39988400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr7:39987800-39988400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr7:39987800-39988400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr7:39987800-39988400	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr7:39987800-39988400	Enhancers	Fetal Heart	heart
12	chr7:39987800-39988400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
13	chr7:39987800-39988400	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr7:39987800-39988400	Flanking Active TSS	Stomach Smooth Muscle	stomach
15	chr7:39987800-39988600	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr7:39987800-39988600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr7:39987800-39988600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr7:39987800-39988800	Active TSS	Right Atrium	heart
19	chr7:39987800-39992800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr7:39987800-39993200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:39987800-39993400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:39988000-39988400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr7:39988000-39988400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr7:39988000-39988400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr7:39988000-39988400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:39988000-39988400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr7:39988000-39988400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr7:39988000-39988400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr7:39988000-39988400	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr7:39988000-39988400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
31	chr7:39988000-39988400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:39988000-39988400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:39988000-39988400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr7:39988000-39988400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr7:39988000-39988400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:39988000-39988400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr7:39988000-39988400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:39988000-39988400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:39988000-39988400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr7:39988000-39988400	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr7:39988000-39988400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr7:39988000-39988400	Flanking Active TSS	Brain Germinal Matrix	brain
43	chr7:39988000-39988400	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr7:39988000-39988400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr7:39988000-39988400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr7:39988000-39988400	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr7:39988000-39988400	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr7:39988000-39988400	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr7:39988000-39988400	Flanking Active TSS	Fetal Muscle Leg	muscle
50	chr7:39988000-39988400	Enhancers	Placenta Amnion	Placenta Amnion

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