Variant report

Variant	rs7979561
Chromosome Location	chr12:124088064-124088065
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:124087994-124088265	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123872223..123875553-chr12:124085591..124088201,3	MCF-7	breast:
2	chr12:124067363..124072745-chr12:124084857..124088217,7	K562	blood:
3	chr12:124084988..124092992-chr12:124114351..124121638,14	K562	blood:
4	chr12:124087290..124089167-chr12:124099421..124102129,2	MCF-7	breast:
5	chr12:123716171..123718231-chr12:124086645..124088616,2	K562	blood:
6	chr12:124085831..124093816-chr12:124094373..124101211,18	MCF-7	breast:
7	chr12:123872056..123874942-chr12:124085224..124088307,3	MCF-7	breast:
8	chr12:124067302..124072457-chr12:124084684..124088760,8	K562	blood:
9	chr12:124086555..124088221-chr12:124100026..124101762,2	K562	blood:
10	chr12:124085449..124088387-chr12:124115552..124120028,6	MCF-7	breast:
11	chr12:124086664..124088557-chr12:124117448..124120033,4	K562	blood:
12	chr12:123847169..123849970-chr12:124085128..124088523,3	K562	blood:

No data

Variant related genes	Relation type
DDX55	TF binding region
ENSG00000206897	Chromatin interaction
ENSG00000111364	Chromatin interaction
ENSG00000086598	Chromatin interaction
ENSG00000139697	Chromatin interaction
ENSG00000111358	Chromatin interaction
ENSG00000247373	Chromatin interaction
ENSG00000051825	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000111361	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000130921	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1050443	0.94[EUR][1000 genomes]
rs1050448	0.86[EUR][1000 genomes]
rs1050449	0.86[EUR][1000 genomes]
rs1056132	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11057301	0.81[EUR][1000 genomes]
rs11833889	0.89[EUR][1000 genomes]
rs12809853	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816883	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12829500	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15587	0.89[EUR][1000 genomes]
rs16917551	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3190835	0.86[EUR][1000 genomes]
rs3204541	0.89[EUR][1000 genomes]
rs34097324	0.89[EUR][1000 genomes]
rs34369761	0.81[EUR][1000 genomes]
rs34514002	0.89[EUR][1000 genomes]
rs35064645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35708602	0.89[EUR][1000 genomes]
rs35867744	0.89[EUR][1000 genomes]
rs36002329	0.97[EUR][1000 genomes]
rs3850952	0.83[EUR][1000 genomes]
rs4930704	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4930709	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930712	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4930713	0.81[EUR][1000 genomes]
rs4930714	0.81[EUR][1000 genomes]
rs55705511	0.86[EUR][1000 genomes]
rs56213464	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56675602	0.89[EUR][1000 genomes]
rs59126974	0.89[EUR][1000 genomes]
rs6488877	0.86[ASN][1000 genomes]
rs6488884	0.85[EUR][1000 genomes]
rs66494087	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66694750	0.89[EUR][1000 genomes]
rs68163141	0.87[EUR][1000 genomes]
rs7137473	0.89[EUR][1000 genomes]
rs7139162	0.89[EUR][1000 genomes]
rs71458807	0.92[EUR][1000 genomes]
rs71458808	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308304	0.89[EUR][1000 genomes]
rs7309292	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313207	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313751	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7398935	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7953876	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956299	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7962151	0.86[ASN][1000 genomes]
rs7963804	0.86[ASN][1000 genomes]
rs7972380	0.81[EUR][1000 genomes]
rs7973766	0.81[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	nsv1050598	chr12:123991646-124214332	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv541623	chr12:123991646-124214332	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
4	nsv1042181	chr12:124037400-124152950	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7979561	TCTN2	cis	Adipose Subcutaneous	GTEx
rs7979561	TCTN2	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124085600-124088400	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr12:124085600-124088400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr12:124085800-124088400	Active TSS	GM12878-XiMat	blood
4	chr12:124087200-124088200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:124087200-124088400	Flanking Active TSS	Dnd41	blood
6	chr12:124087400-124088400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:124087400-124088400	Flanking Active TSS	Hela-S3	cervix
8	chr12:124087600-124088200	Enhancers	Primary B cells from peripheral blood	blood
9	chr12:124087600-124088200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:124087600-124088400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:124087600-124088400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr12:124087600-124088400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:124087600-124088400	Enhancers	Placenta	Placenta
14	chr12:124087600-124088600	Enhancers	Fetal Brain Male	brain
15	chr12:124087600-124091800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr12:124087800-124088200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:124087800-124088200	Weak transcription	Fetal Intestine Small	intestine
18	chr12:124087800-124088200	Enhancers	Thymus	Thymus
19	chr12:124087800-124088400	Enhancers	Primary B cells from cord blood	blood
20	chr12:124087800-124088400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr12:124087800-124088400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:124087800-124088400	Enhancers	Brain Angular Gyrus	brain
23	chr12:124087800-124088400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr12:124087800-124088400	Weak transcription	Left Ventricle	heart
25	chr12:124087800-124088400	Weak transcription	Ovary	ovary
26	chr12:124087800-124088600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:124087800-124088600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:124087800-124088600	Enhancers	Primary T cells fromperipheralblood	blood
29	chr12:124087800-124088600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr12:124087800-124088600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:124087800-124088600	Weak transcription	Pancreas	Pancrea
32	chr12:124087800-124088600	Weak transcription	Spleen	Spleen
33	chr12:124087800-124088600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr12:124087800-124088800	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:124087800-124088800	Weak transcription	NH-A	brain
36	chr12:124087800-124089200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr12:124087800-124089400	Weak transcription	HSMMtube	muscle
38	chr12:124087800-124089600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:124087800-124089600	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:124087800-124089600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:124087800-124089800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:124087800-124090000	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:124087800-124090200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:124087800-124090200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr12:124087800-124090200	Weak transcription	Esophagus	oesophagus
46	chr12:124087800-124090200	Weak transcription	Right Ventricle	heart
47	chr12:124087800-124090400	Weak transcription	Fetal Kidney	kidney
48	chr12:124087800-124090600	Weak transcription	Psoas Muscle	Psoas
49	chr12:124087800-124091200	Weak transcription	Colonic Mucosa	Colon
50	chr12:124087800-124091200	Weak transcription	Colon Smooth Muscle	Colon

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