Variant report

Variant	rs12953178
Chromosome Location	chr17:37617008-37617009
allele	A/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	ZBTB33	chr17:37616826-37619498	A549	lung:	n/a	chr17:37617697-37617712
2	POLR2A	chr17:37616905-37617127	HepG2	liver:	n/a	n/a
3	ZNF384	chr17:37616930-37618170	K562	blood:	n/a	n/a
4	HCFC1	chr17:37616733-37619510	Hela-S3	cervix:	n/a	n/a
5	TCF12	chr17:37616839-37618713	A549	lung:	n/a	chr17:37617747-37617754
6	SIX5	chr17:37616964-37618219	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:37604386..37611889-chr17:37616048..37620931,25	K562	blood:
2	chr17:37353026..37355461-chr17:37616658..37619340,2	MCF-7	breast:
3	chr17:37615177..37617856-chr19:59063174..59065856,2	MCF-7	breast:
4	chr17:37604313..37610125-chr17:37615155..37621784,15	MCF-7	breast:
5	chr17:37605291..37610010-chr17:37614517..37620203,14	MCF-7	breast:
6	chr17:37604291..37611614-chr17:37614953..37621274,26	K562	blood:

Variant related genes	Relation type
CDK12	TF binding region
ENSG00000067191	Chromatin interaction
ENSG00000125686	Chromatin interaction
ENSG00000130724	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12940109	1.00[AMR][1000 genomes]
rs12940881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12940956	1.00[AMR][1000 genomes]
rs12943456	1.00[EUR][1000 genomes]
rs12944298	1.00[EUR][1000 genomes]
rs12945363	1.00[AMR][1000 genomes]
rs12947238	1.00[AMR][1000 genomes]
rs12950784	1.00[EUR][1000 genomes]
rs34821956	1.00[AMR][1000 genomes]
rs34904106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34910003	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34983824	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35194764	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35269184	1.00[AMR][1000 genomes]
rs35366897	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35499078	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35550184	1.00[EUR][1000 genomes]
rs35598597	1.00[EUR][1000 genomes]
rs35656573	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35821333	1.00[EUR][1000 genomes]
rs35829705	1.00[AMR][1000 genomes]
rs35853230	1.00[AMR][1000 genomes]
rs35896550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4252626	1.00[EUR][1000 genomes]
rs4988981	1.00[EUR][1000 genomes]
rs57059040	1.00[EUR][1000 genomes]
rs57938769	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58452873	1.00[EUR][1000 genomes]
rs59775294	1.00[AMR][1000 genomes]
rs6503512	1.00[AMR][1000 genomes]
rs71369747	0.83[AMR][1000 genomes]
rs71369760	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369763	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71369767	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs71369773	1.00[EUR][1000 genomes]
rs71577045	0.83[AMR][1000 genomes]
rs7212530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7212780	1.00[AMR][1000 genomes]
rs7218668	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7219611	1.00[EUR][1000 genomes]
rs7219683	1.00[EUR][1000 genomes]
rs7226222	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8064372	1.00[AMR][1000 genomes]
rs8069194	1.00[AMR][1000 genomes]
rs8073144	1.00[AMR][1000 genomes]
rs8074199	1.00[AMR][1000 genomes]
rs8076843	1.00[AMR][1000 genomes]
rs8077259	1.00[AMR][1000 genomes]
rs8077822	1.00[AMR][1000 genomes]
rs8079346	1.00[AMR][1000 genomes]
rs8080830	1.00[AMR][1000 genomes]
rs8081561	1.00[AMR][1000 genomes]
rs9747574	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9747666	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1060126	chr17:37333956-37659189	Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv1057655	chr17:37333956-37732451	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
5	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
6	nsv908204	chr17:37349655-37682657	Genic enhancers Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv1057057	chr17:37395082-37627025	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
10	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
11	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
12	nsv1063848	chr17:37575622-37707592	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37608400-37617200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr17:37608600-37617200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr17:37616800-37617200	Enhancers	Primary B cells from cord blood	blood
4	chr17:37616800-37617200	Enhancers	Primary B cells from peripheral blood	blood
5	chr17:37616800-37617200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr17:37616800-37617200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
7	chr17:37616800-37617200	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr17:37616800-37617200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr17:37616800-37617200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr17:37616800-37617200	Enhancers	Esophagus	oesophagus
11	chr17:37616800-37619200	Active TSS	Brain Hippocampus Middle	brain
12	chr17:37616800-37619200	Active TSS	A549	lung
13	chr17:37616800-37619600	Active TSS	Brain Anterior Caudate	brain
14	chr17:37616800-37620400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr17:37616800-37620400	Active TSS	Stomach Smooth Muscle	stomach
16	chr17:37617000-37617200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr17:37617000-37617200	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr17:37617000-37617200	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr17:37617000-37617200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:37617000-37617200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr17:37617000-37617200	Enhancers	Fetal Muscle Trunk	muscle
22	chr17:37617000-37617200	Enhancers	Fetal Muscle Leg	muscle
23	chr17:37617000-37617200	Flanking Active TSS	Placenta	Placenta
24	chr17:37617000-37617200	Enhancers	Gastric	stomach
25	chr17:37617000-37617200	Enhancers	Lung	lung
26	chr17:37617000-37617200	Weak transcription	Right Ventricle	heart
27	chr17:37617000-37617200	Enhancers	GM12878-XiMat	blood
28	chr17:37617000-37617200	Enhancers	HUVEC	blood vessel
29	chr17:37617000-37617400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr17:37617000-37617400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr17:37617000-37617400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:37617000-37617400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr17:37617000-37617400	Flanking Active TSS	Liver	Liver
34	chr17:37617000-37617400	Flanking Active TSS	Dnd41	blood
35	chr17:37617000-37617400	Flanking Active TSS	HepG2	liver
36	chr17:37617000-37617800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr17:37617000-37618400	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr17:37617000-37618400	Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr17:37617000-37618400	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr17:37617000-37618600	Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr17:37617000-37618600	Active TSS	Adipose Nuclei	Adipose
42	chr17:37617000-37618800	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr17:37617000-37618800	Active TSS	Duodenum Mucosa	Duodenum
44	chr17:37617000-37618800	Active TSS	Thymus	Thymus
45	chr17:37617000-37619000	Active TSS	Brain Substantia Nigra	brain
46	chr17:37617000-37619000	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr17:37617000-37619400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:37617000-37619400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr17:37617000-37619600	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr17:37617000-37619800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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