Variant report

Variant	rs6782164
Chromosome Location	chr3:42620684-42620685
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	POLR2A	chr3:42620445-42620692	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:42540384..42544045-chr3:42620631..42622853,3	K562	blood:
2	chr3:42620456..42625490-chr3:42691753..42697487,7	K562	blood:
3	chr3:42619900..42621497-chr3:42638395..42640003,2	MCF-7	breast:

Variant related genes	Relation type
SS18L2	TF binding region
ENSG00000230084	Chromatin interaction
ENSG00000114812	Chromatin interaction
ENSG00000114853	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1062051	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13085695	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13089845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13090902	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13093680	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13095447	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17074662	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17074673	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17074674	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17074693	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2284303	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2284304	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300057	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300058	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2302352	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33969824	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs33984028	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683820	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34687113	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34762478	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34801786	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34852409	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34977988	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35676838	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36033201	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774402	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774404	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3774407	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3821836	0.85[ASN][1000 genomes]
rs3846058	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3846059	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3856737	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3886782	0.87[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57259216	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58868911	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59914338	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60232916	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60348477	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441928	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66786953	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67059259	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67533173	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.88[ASN][1000 genomes]
rs6778982	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795296	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs68071013	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72864072	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7617736	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42603000-42622800	Weak transcription	Colonic Mucosa	Colon
2	chr3:42604200-42622800	Weak transcription	Psoas Muscle	Psoas
3	chr3:42604200-42623000	Weak transcription	Esophagus	oesophagus
4	chr3:42604600-42622400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr3:42605000-42621400	Weak transcription	HMEC	breast
6	chr3:42605200-42622400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:42607800-42621600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:42607800-42622800	Weak transcription	Pancreas	Pancrea
9	chr3:42608000-42623000	Weak transcription	Gastric	stomach
10	chr3:42608600-42621400	Weak transcription	Brain Hippocampus Middle	brain
11	chr3:42608600-42622800	Weak transcription	Aorta	Aorta
12	chr3:42609000-42621600	Weak transcription	NHLF	lung
13	chr3:42609000-42622800	Weak transcription	HSMMtube	muscle
14	chr3:42609000-42623000	Weak transcription	Spleen	Spleen
15	chr3:42609200-42621200	Weak transcription	Colon Smooth Muscle	Colon
16	chr3:42609200-42621600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:42609200-42621600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:42609200-42621800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:42609200-42622400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:42609600-42623000	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:42610000-42622000	Weak transcription	Osteobl	bone
22	chr3:42610400-42622600	Weak transcription	Right Ventricle	heart
23	chr3:42610600-42622200	Weak transcription	NH-A	brain
24	chr3:42610600-42623000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:42611000-42621800	Weak transcription	Liver	Liver
26	chr3:42611200-42621600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:42611200-42622000	Weak transcription	Brain Substantia Nigra	brain
28	chr3:42611400-42621800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:42611400-42622800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:42611600-42621200	Weak transcription	HepG2	liver
31	chr3:42611600-42621600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:42611600-42622800	Weak transcription	Ovary	ovary
33	chr3:42611800-42621600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:42611800-42621800	Weak transcription	Fetal Heart	heart
35	chr3:42614200-42621800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr3:42614200-42622200	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:42614200-42622800	Weak transcription	Left Ventricle	heart
38	chr3:42615000-42623000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:42615000-42623000	Weak transcription	Lung	lung
40	chr3:42615200-42622600	Weak transcription	Thymus	Thymus
41	chr3:42615600-42621400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr3:42616200-42621600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:42616600-42622600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:42616600-42622600	Weak transcription	Fetal Stomach	stomach
45	chr3:42616600-42622800	Weak transcription	Placenta	Placenta
46	chr3:42616800-42622000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:42616800-42622200	Weak transcription	Fetal Intestine Large	intestine
48	chr3:42617000-42621800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr3:42617000-42622400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:42617200-42621200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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